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Bernardi S, Vallati M, Gatta R. Artificial Intelligence-Based Management of Adult Chronic Myeloid Leukemia: Where Are We and Where Are We Going? Cancers (Basel) 2024; 16:848. [PMID: 38473210 DOI: 10.3390/cancers16050848] [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: 01/18/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Artificial intelligence (AI) is emerging as a discipline capable of providing significant added value in Medicine, in particular in radiomic, imaging analysis, big dataset analysis, and also for generating virtual cohort of patients. However, in coping with chronic myeloid leukemia (CML), considered an easily managed malignancy after the introduction of TKIs which strongly improved the life expectancy of patients, AI is still in its infancy. Noteworthy, the findings of initial trials are intriguing and encouraging, both in terms of performance and adaptability to different contexts in which AI can be applied. Indeed, the improvement of diagnosis and prognosis by leveraging biochemical, biomolecular, imaging, and clinical data can be crucial for the implementation of the personalized medicine paradigm or the streamlining of procedures and services. In this review, we present the state of the art of AI applications in the field of CML, describing the techniques and objectives, and with a general focus that goes beyond Machine Learning (ML), but instead embraces the wider AI field. The present scooping review spans on publications reported in Pubmed from 2003 to 2023, and resulting by searching "chronic myeloid leukemia" and "artificial intelligence". The time frame reflects the real literature production and was not restricted. We also take the opportunity for discussing the main pitfalls and key points to which AI must respond, especially considering the critical role of the 'human' factor, which remains key in this domain.
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Affiliation(s)
- Simona Bernardi
- Department of Clinical and Experimental Sciences, University of Brescia, 25123 Brescia, Italy
- CREA-Centro di Ricerca Emato-Oncologica AIL, ASST Spedali Civili of Brescia, 25123 Brescia, Italy
| | - Mauro Vallati
- School of Computing and Engineering, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Roberto Gatta
- Department of Clinical and Experimental Sciences, University of Brescia, 25123 Brescia, Italy
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Naveed M, Ali N, Aziz T, Hanif N, Fatima M, Ali I, Alharbi M, Alasmari AF, Albekairi TH. The natural breakthrough: phytochemicals as potent therapeutic agents against spinocerebellar ataxia type 3. Sci Rep 2024; 14:1529. [PMID: 38233440 PMCID: PMC10794461 DOI: 10.1038/s41598-024-51954-3] [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: 11/07/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
There is no FDA-approved drug for neurological disorders like spinocerebellar ataxia type 3. CAG repeats mutation in the ATXN3 gene, causing spinocerebellar ataxia type 3 disease. Symptoms include sleep cycle disturbance, neurophysiological abnormalities, autonomic dysfunctions, and depression. This research focuses on drug discovery against ATXN3 using phytochemicals of different plants. Three phytochemical compounds (flavonoids, diterpenoids, and alkaloids) were used as potential drug candidates and screened against the ATXN3 protein. The 3D structure of ATXN3 protein and phytochemicals were retrieved and validation of the protein was 98.1% Rama favored. The protein binding sites were identified for the interaction by CASTp. ADMET was utilized for the pre-clinical analysis, including solubility, permeability, drug likeliness and toxicity, and chamanetin passed all the ADMET properties to become a lead drug candidate. Boiled egg analysis attested that the ligand could cross the gastrointestinal tract. Pharmacophore analysis showed that chamanetin has many hydrogen acceptors and donors which can form interaction bonds with the receptor proteins. Chamanetin passed all the screening analyses, having good absorption, no violation of Lipinski's rule, nontoxic properties, and good pharmacophore properties. Chamanetin was one of the lead compounds with a - 7.2 kcal/mol binding affinity after screening the phytochemicals. The stimulation of ATXN3 showed stability after 20 ns of interaction in an overall 50 ns MD simulation. Chamanetin (Flavonoid) was predicted to be highly active against ATXN3 with good drug-like properties. In-silico active drug against ATXN3 from a plant source and good pharmacokinetics parameters would be excellent drug therapy for SC3, such as flavonoids (Chamanetin).
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Pakistan.
| | - Nouman Ali
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Pakistan
| | - Tariq Aziz
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, University of Ioannina, 47100, Arta, Greece.
| | - Nimra Hanif
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Pakistan
| | - Mahnoor Fatima
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Pakistan
| | - Imran Ali
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Thamer H Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
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Sarkar K, Nandi S, Das RK. Computational insights into pediatric adenovirus inhibitors: in silico strategies for drug repurposing. J Biomol Struct Dyn 2023:1-14. [PMID: 37642990 DOI: 10.1080/07391102.2023.2252072] [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: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Human adenovirus (HADV) infection can pose a serious threat to children, leading to a variety of respiratory illnesses and other complications. Particularly, children with weak immune systems are vulnerable to severe adenovirus infections with high mortality. The main focus of this study is to propose new antiviral agents as lead HADV inhibitors for children. So, several antiviral agents used in children were subjected to finding new HADV inhibitors using important computational methods of molecular docking, molecular dynamics (MD) simulation, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding free energy calculations, density functional theory (DFT), and pharmacokinetic analysis. Molecular docking of standard cidofovir along with other ligands, suggested that sofosbuvir has the highest binding energy (-10.8 kcal/mol), followed by baloxavir marboxil (-10.36 kcal/mol). Further, the analysis of molecular interactions using MD simulation (100 ns) and MM-PBSA indicated that baloxavir marboxil has formed the most stable protein-ligand complex with HADV, followed by sofosbuvir. The binding free energies of baloxavir marboxil and sofosbuvir were found to be -61.724 kJ/mol and -48.123 kJ/mol, respectively. The DFT and drug-likeness properties of these compounds were also investigated. Overall, two antiviral agents, such as baloxavir marboxil, and sofosbuvir are suggested as lead repurposed candidates against HADV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kaushik Sarkar
- Department of Chemistry, University of North Bengal, Darjeeling, West Bengal, India
| | - Subrata Nandi
- Department of Chemistry, University of North Bengal, Darjeeling, West Bengal, India
| | - Rajesh Kumar Das
- Department of Chemistry, University of North Bengal, Darjeeling, West Bengal, India
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Raza AR, Rubab SL, Ashfaq M, Altaf Y, Tahir MN, Rehman MFU, Aziz T, Alharbi M, Alasmari AF. Evaluation of Antimicrobial, Anticholinesterase Potential of Indole Derivatives and Unexpectedly Synthesized Novel Benzodiazine: Characterization, DFT and Hirshfeld Charge Analysis. Molecules 2023; 28:5024. [PMID: 37446687 DOI: 10.3390/molecules28135024] [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: 05/13/2023] [Revised: 06/07/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
The pharmacological effectiveness of indoles, benzoxazepines and benzodiazepines initiated our synthesis of indole fused benoxazepine/benzodiazepine heterocycles, along with enhanced biological usefulness of the fused rings. Activated indoles 5, 6 and 7 were synthesized using modified Bischler indole synthesis rearrangement. Indole 5 was substituted with the trichloroacetyl group at the C7 position, yielding 8, exclusively due to the increased nucleophilic character of C7. When trichloroacylated indole 8 was treated with basified ethanol or excess amminia, indole acid 9 and amide 10 were yielded, respectively. Indole amide 10 was expected to give indole fused benoxazepine/benzodiazepine 11a/11b on treatment with alpha halo ester followed by a coupling agent, but when the reaction was tried, an unexpectedly rearranged novel product, 1,3-bezodiazine 12, was obtained. The synthetic compounds were screened for anticholinesterase and antibacterial potential; results showed all products to be very important candidates for both activities, and their potential can be explored further. In addition, 1,3-bezodiazine 12 was explored by DFT studies, Hirshfeld surface charge analysis and structural insight to obrain a good picture of the structure and reactivity of the products for the design of derivatised drugs from the novel compound.
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Affiliation(s)
- Abdul Rauf Raza
- Institute of Chemistry, Ibn e Sina Block, University of Sargodha, Sargodha 40100, Pakistan
| | - Syeda Laila Rubab
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Muhammad Ashfaq
- Department of Physics, University of Sargodha, Sargodha 40100, Pakistan
| | - Yasir Altaf
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | | | | | - Tariq Aziz
- Department of Agriculture, University of Ioannina, 471 32 Arta, Greece
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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