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Aminu KS, Uzairu A, Abechi SE, Shallangwa GA, Umar AB. Activity prediction, structure-based drug design, molecular docking, and pharmacokinetic studies of 1,4-dihydropyridines derivatives as α-amylase inhibitors. J Taibah Univ Med Sci 2024; 19:270-286. [PMID: 38234713 PMCID: PMC10793175 DOI: 10.1016/j.jtumed.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/16/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024] Open
Abstract
Objectives Diabetes places a substantial economic burden on countries worldwide. The costs associated with diabetes management, including healthcare services, medications, monitoring equipment, and productivity losses, are substantial. The International Diabetes Federation has estimated that global healthcare expenditures associated with diabetes and its complications exceed hundreds of billions of dollars annually. Therefore, a critical need exists to develop drugs that are highly effective, affordable, and easily accessible to society. Methods This study explored the structural modification of 1,4-DHP derivatives to identify specific α-amylase inhibitors, with the aim of developing more effective and accessible drugs for diabetes. We evaluated the activity and binding ability of the designed compounds. In addition, we performed drug-likeness and pharmacokinetic studies on the modified compounds. Results Equation (1) had the highest accuracy, on the basis of internal and external assessment parameters, including R2int = 0.852, R2adj = 0.803, Q2cv = 0.731, and R2ext = 0.884. Moreover, the five potent analogs identified through structure-based drug design demonstrated a more favorable interaction than observed for the template or acarbose. Additionally, comprehensive studies on the drug-like properties and pharmacokinetics of the designed compounds supported their oral safety and favorable pharmacokinetic profiles. Conclusions The designed analogs show promise for developing new hypoglycemic agents. Their positive attributes and performance suggest that they may potentially serve as candidates for further research in improving treatments for high blood sugar-associated conditions.
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Affiliation(s)
- Khalifa S. Aminu
- Department of Chemistry, Ahmadu Bello University, Zaria, Nigeria
- Department of Pure and Industrial Chemistry, Bayero University, Kano, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Ahmadu Bello University, Zaria, Nigeria
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Hammouda MM, Gaffer HE, Elattar KM. Insights into the medicinal chemistry of heterocycles integrated with a pyrazolo[1,5- a]pyrimidine scaffold. RSC Med Chem 2022; 13:1150-1196. [PMID: 36325400 PMCID: PMC9580358 DOI: 10.1039/d2md00192f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/25/2022] [Indexed: 09/10/2023] Open
Abstract
Pyrazolo[1,5-a]pyrimidines are the dominant motif of many drugs; for instance, zaleplon and indiplon are sedative agents and ocinaplon was identified as an anxiolytic agent. The importance of this class of compounds lies in its varied and significant biological activities, and accordingly, considerable methods have been devised to prepare these compounds. Hence, other derivatives of this class of compounds were prepared by substitution reactions with different nucleophiles exploiting the activity of groups linked to the ring carbon and nitrogen atoms. The methods used vary through the condensation reactions of the aminopyrazoles with 1,2-allenic, enaminonitriles, enaminones, 1,3-diketones, unsaturated nitriles, or unsaturated ketones. Alternatively, these compounds are prepared through the reactions of acyclic reagents, as these methods were recently developed efficiently with high yields. The current review highlighted the recent progress of the therapeutic potential of pyrazolo[1,5-a]pyrimidines as antimicrobial, anticancer, antianxiety, anti-proliferative, analgesic, and antioxidant agents, carboxylesterase, translocator protein and PDE10A inhibitors, and selective kinase inhibitors.
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Affiliation(s)
- Mohamed M Hammouda
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University Al-Kharj 11942 Saudi Arabia
- Chemistry Department, Faculty of Science, Mansoura University El-Gomhoria Street Mansoura 35516 Egypt
| | - Hatem E Gaffer
- Dyeing and Printing Department, Textile Research Division, National Research Center Dokki Cairo 12622 Egypt
| | - Khaled M Elattar
- Unit of Genetic Engineering and Biotechnology, Faculty of Science, Mansoura University El-Gomhoria Street Mansoura 35516 Egypt +201010655354
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Shayanfar S, Shayanfar A. Comparison of various methods for validity evaluation of QSAR models. BMC Chem 2022; 16:63. [PMID: 35999611 PMCID: PMC9396839 DOI: 10.1186/s13065-022-00856-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Quantitative structure-activity relationship (QSAR) modeling is one of the most important computational tools employed in drug discovery and development. The external validation of QSAR models is the main point to check the reliability of developed models for the prediction activity of not yet synthesized compounds. It was performed by different criteria in the literature. METHODS In this study, 44 reported QSAR models for biologically active compounds reported in scientific papers were collected. Various statistical parameters of external validation of a QSAR model were calculated, and the results were discussed. RESULTS The findings revealed that employing the coefficient of determination (r2) alone could not indicate the validity of a QSAR model. The established criteria for external validation have some advantages and disadvantages which should be considered in QSAR studies. CONCLUSION This study showed that these methods alone are not only enough to indicate the validity/invalidity of a QSAR model.
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Affiliation(s)
- Shadi Shayanfar
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shayanfar
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Editorial Office of Pharmaceutical Sciences Journal, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Walhekar V, Bagul C, Kumar D, Muthal A, Achaiah G, Kulkarni R. Topical advances in PIM kinases and their inhibitors: Medicinal chemistry perspectives. Biochim Biophys Acta Rev Cancer 2022; 1877:188725. [DOI: 10.1016/j.bbcan.2022.188725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/28/2022]
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Ghaleb A, Aouidate A, Ayouchia HBE, Aarjane M, Anane H, Stiriba SE. In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADMET screening. J Biomol Struct Dyn 2020; 40:143-153. [PMID: 32799761 DOI: 10.1080/07391102.2020.1808530] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The new coronavirus SARS-CoV-2 virus is causing a severe pneumonia in human, provoking the serious outbreak epidemic CoV-2. Since its appearance in Wuhan, China on December 2019, CoV-2 becomes the biggest challenge the world is facing today, including the discovery of antiviral drug for SARS-CoV-2. In this study, the potential inhibitory of a class of human SARS inhibitors, namely pyridine N-oxide derivatives, against CoV-2 was addressed by quantitative structure-activity relationship 3 D-QSAR. The reliable CoMSIA developed model of 110 pyridine N-oxide based-antiviral compounds, showed Q2= 0.54 and rext2=0.71. The molecular surflex-docking was applied to identify the crystal structure of CoV-2 main protease 3CLpro (PDB: 6LU7) and two potentially and largely used antiviral molecules, namely chloroquine, hydroxychloroquine. The obtained free energy affinity and ADMET properties indicate that among the series of model antiviral compounds examined, the new antiviral compound A5 could be an excellent antiviral drug inhibitor against COVID-19. The inhibition activity of pyridine N-oxyde compounds against CoV-2 was compared with the activity of two common antiviral drug, namely chloroquine (CQ) and hydroxychloroquine (HCQ). DFT method was also used to define the sites of reactivity of pyridine N-oxyde derivatives as well as CQ and HCQ.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adib Ghaleb
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Adnane Aouidate
- MCNSL, School of Sciences, Moulay Ismail University, Meknes, Morocco
| | - Hicham Ben El Ayouchia
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Mohammed Aarjane
- LCBAE, Equipe Chimie Moléculaire et Molécules Bioactives, Université Moulay Ismail, Faculté des Sciences, Meknès, Morocco
| | - Hafid Anane
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco
| | - Salah-Eddine Stiriba
- Laboratoire de Chimie Analytique et Moléculaire/LCAM, Faculté Polydisciplinaire de Safi, Université Cadi Ayyad, Safi, Morocco.,Instituto de Ciencia Molecular/ICMol, Universidad de Valencia, Valencia, Spain
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Aouidate A, Ghaleb A, Chtita S, Aarjane M, Ousaa A, Maghat H, Sbai A, Choukrad M, Bouachrine M, Lakhlifi T. Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation. J Biomol Struct Dyn 2020; 39:4522-4535. [PMID: 32552534 PMCID: PMC7309310 DOI: 10.1080/07391102.2020.1779130] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected whole the world with more than 6 million confirmed cases and over 370,000 deaths. At present, there are no effective treatments or vaccine for this disease, which constitutes a serious global health crisis. As the pandemic still spreading around the globe, it is of interest to use computational methods to identify potential inhibitors for the virus. The crystallographic structures of 3CLpro (PDB: 6LU7) and RdRp (PDB 6ML7) were used in virtual screening of 50000 chemical compounds obtained from the CAS Antiviral COVID19 database using 3D-similarity search and standard molecular docking followed by ranking and selection of compounds based on their binding affinity, computational techniques for the sake of details on the binding interactions, absorption, distribution, metabolism, excretion, and toxicity prediction; we report three 4-(morpholin-4-yl)-1,3,5-triazin-2-amine derivatives; two compounds (2001083-68-5 and 2001083-69-6) with optimal binding features to the active site of the main protease and one compound (833463-19-7) with optimal binding features to the active site of the polymerase for further consideration to fight COVID-19. The structural stability and dynamics of lead compounds at the active site of 3CLpro and RdRp were examined using molecular dynamics (MD) simulation. Essential dynamics demonstrated that the three complexes remain stable during simulation of 20 ns, which may be suitable candidates for further experimental analysis. As the identified leads share the same scaffold, they may serve as promising leads in the development of dual 3CLpro and RdRp inhibitors against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adnane Aouidate
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Adib Ghaleb
- Laboratory of Analytical and Molecular Chemistry (LCAM), Polydisciplinary Faculty, Cadi Ayyad University, Safi, Morocco
| | - Samir Chtita
- Laboratory physical of chemistry of materials, Faculty of sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohammed Aarjane
- LCBAE, Faculty of Science, University Moulay Ismail, Meknes, Morocco
| | - Abdellah Ousaa
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Hamid Maghat
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - M'barek Choukrad
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco.,Est Khenifra, Sultan Moulay Sliman University, Beni Mellal, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University, Meknes, Morocco
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Ancuceanu R, Dinu M, Neaga I, Laszlo FG, Boda D. Development of QSAR machine learning-based models to forecast the effect of substances on malignant melanoma cells. Oncol Lett 2019; 17:4188-4196. [PMID: 31007759 PMCID: PMC6466999 DOI: 10.3892/ol.2019.10068] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
SK-MEL-5 is a human melanoma cell line that has been used in various studies to explore new therapies against melanoma in different in vitro experiments. Based on this study we report on the development of quantitative structure-activity relationship (QSAR) models able to predict the cytotoxic effect of diverse chemical compounds on this cancer cell line. The dataset of cytotoxic and inactive compounds were downloaded from the PubChem database. It contains the data for all chemical compounds for which cytotoxicity results expressed by GI50 was recorded. In total 13 blocks of molecular descriptors were computed and used, after appropriate pre-processing in building QSAR models with four machine learning classifiers: Random forest (RF), gradient boosting, support vector machine and random k-nearest neighbors. Among the 186 models reported none had a positive predictive value (PPV) higher than 0.90 in both nested cross-validation and on an external dataset testing, but 7 models had a PPV higher than 0.85 in both evaluations, all seven using the RFs algorithm as a classifier, and topological descriptors, information indices, 2D-autocorrelation descriptors, P-VSA-like descriptors, and edge-adjacency descriptors as sets of features used for classification. The y-scrambling test was associated with considerably worse performance (confirming the non-random character of the models) and the applicability domain was assessed through three different methods.
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Affiliation(s)
- Robert Ancuceanu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, 'Carol Davila' University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Mihaela Dinu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, 'Carol Davila' University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Iana Neaga
- Department of Public Health and Management, Faculty of Medicine, 'Carol Davila' University of Medicine and Pharmacy, 050463 Bucharest, Romania
| | - Fekete Gyula Laszlo
- Department of Dermatology, University of Medicine and Pharmacy of Târgu Mureş, 540142 Târgu Mureş, Romania
| | - Daniel Boda
- Dermatology Research Laboratory, 'Carol Davila' University of Medicine and Pharmacy, 050474 Bucharest, Romania
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