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Kibet S, Kimani NM, Mwanza SS, Mudalungu CM, Santos CBR, Tanga CM. Unveiling the Potential of Ent-Kaurane Diterpenoids: Multifaceted Natural Products for Drug Discovery. Pharmaceuticals (Basel) 2024; 17:510. [PMID: 38675469 DOI: 10.3390/ph17040510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Natural products hold immense potential for drug discovery, yet many remain unexplored in vast libraries and databases. In an attempt to fill this gap and meet the growing demand for effective drugs, this study delves into the promising world of ent-kaurane diterpenoids, a class of natural products with huge therapeutic potential. With a dataset of 570 ent-kaurane diterpenoids obtained from the literature, we conducted an in silico analysis, evaluating their physicochemical, pharmacokinetic, and toxicological properties with a focus on their therapeutic implications. Notably, these natural compounds exhibit drug-like properties, aligning closely with those of FDA-approved drugs, indicating a high potential for drug development. The ranges of the physicochemical parameters were as follows: molecular weights-288.47 to 626.82 g/mol; number of heavy atoms-21 to 44; the number of hydrogen bond donors and acceptors-0 to 8 and 1 to 11, respectively; the number of rotatable bonds-0 to 11; fraction Csp3-0.65 to 1; and TPSA-20.23 to 189.53 Ų. Additionally, the majority of these molecules display favorable safety profiles, with only 0.70%, 1.40%, 0.70%, and 46.49% exhibiting mutagenic, tumorigenic, reproduction-enhancing, and irritant properties, respectively. Importantly, ent-kaurane diterpenoids exhibit promising biopharmaceutical properties. Their average lipophilicity is optimal for drug absorption, while over 99% are water-soluble, facilitating delivery. Further, 96.5% and 28.20% of these molecules exhibited intestinal and brain bioavailability, expanding their therapeutic reach. The predicted pharmacological activities of these compounds encompass a diverse range, including anticancer, immunosuppressant, chemoprotective, anti-hepatic, hepatoprotectant, anti-inflammation, antihyperthyroidism, and anti-hepatitis activities. This multi-targeted profile highlights ent-kaurane diterpenoids as highly promising candidates for further drug discovery endeavors.
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Affiliation(s)
- Shadrack Kibet
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Njogu M Kimani
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya
| | - Syombua S Mwanza
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Cynthia M Mudalungu
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
- School of Chemistry and Material Science, The Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
| | - Cleydson B R Santos
- Graduate Program in Medicinal Chemistry and Molecular Modelling, Health Science Institute, Federal University of Pará, Belém 66075-110, Brazil
- Laboratory of Modelling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil
| | - Chrysantus M Tanga
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
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Sonker P, Tamang R, Mehata AK, Nidhar M, Sharma VP, Kumar V, Muthu MS, Koch B, Tewari AK. PTSA-induced synthesis, in silico and nano study of novel ethylquinolin-thiazolo-triazole in cervical cancer. Future Med Chem 2024. [PMID: 38596902 DOI: 10.4155/fmc-2023-0344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Aim: p-Toluenesulfonic acid-(PTSA) and grinding-induced novel synthesis of ethylquinolin-thiazolo-triazole derivatives was performed using green chemistry. Materials & methods: Development of a nanoconjugate drug-delivery system of ethylquinolin-thiazolo-triazole was carried out with D-α-tocopheryl polyethylene glycol succinate (TPGS) and the formulation was further characterized by transmission electron microscopy, atomic force microscopy, dynamic light scattering and in vitro drug release assay. The effect of 3a nanoparticles was assessed against a cervical cancer cell line (HeLa) through the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, and the effect on apoptosis was determined. Results & discussion: The 3a nanoparticles triggered the apoptotic mode of cell death after increasing the intracellular reactive oxygen level by enhancing cellular uptake of micelles. Furthermore, in silico studies revealed higher absorption, distribution, metabolism, elimination and toxicity properties and bioavailability of the enzyme tyrosine protein kinase. Conclusion: The 3a nanoparticles enhanced the therapeutic potential and have higher potential for targeted drug delivery against cervical cancer.
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Affiliation(s)
- Priyanka Sonker
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Rupen Tamang
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Abhishesh K Mehata
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Manisha Nidhar
- Amrita school of pharmacy, Amrita Vishwa Vidhyapeetham, AIMS, Health Science Campus, Kochi, 682041, India
| | - Vishal P Sharma
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Vipin Kumar
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Madaswamy S Muthu
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Biplob Koch
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ashish K Tewari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
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El Abbouchi A, Mkhayar K, Elkhattabi S, El Brahmi N, Hiebel MA, Bignon J, Guillaumet G, Suzenet F, El Kazzouli S. Design, Synthesis, Computational Studies, and Anti-Proliferative Evaluation of Novel Ethacrynic Acid Derivatives Containing Nitrogen Heterocycle, Urea, and Thiourea Moieties as Anticancer Agents. Molecules 2024; 29:1437. [PMID: 38611717 PMCID: PMC11013014 DOI: 10.3390/molecules29071437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
In the present work, the synthesis of new ethacrynic acid (EA) derivatives containing nitrogen heterocyclic, urea, or thiourea moieties via efficient and practical synthetic procedures was reported. The synthesised compounds were screened for their anti-proliferative activity against two different cancer cell lines, namely, HL60 (promyelocytic leukaemia) and HCT116 (human colon carcinoma). The results of the in vitro tests reveal that compounds 1-3, 10, 16(a-c), and 17 exhibit potent anti-proliferative activity against the HL60 cell line, with values of the percentage of cell viability ranging from 20 to 35% at 1 μM of the drug and IC50 values between 2.37 μM and 0.86 μM. Compounds 2 and 10 showed a very interesting anti-proliferative activity of 28 and 48% at 1 μM, respectively, against HCT116. Two PyTAP-based fluorescent EA analogues were also synthesised and tested, showing good anti-proliferative activity. A test on the drug-likeness properties in silico of all the synthetised compounds was performed in order to understand the mechanism of action of the most active compounds. A molecular docking study was conducted on two human proteins, namely, glutathione S-transferase P1-1 (pdb:2GSS) and caspase-3 (pdb:4AU8) as target enzymes. The docking results show that compounds 2 and 3 exhibit significant binding modes with these enzymes. This finding provides a potential strategy towards developing anticancer agents, and most of the synthesised and newly designed compounds show good drug-like properties.
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Affiliation(s)
- Abdelmoula El Abbouchi
- Euromed Research Center, Euromed Faculty of Pharmacy, School of Engineering in Biomedical and Biotechnology, Euromed University of Fes (UEMF), Meknes Road, Fez 30000, Morocco; (A.E.A.); (N.E.B.)
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, BP 6759, CEDEX 2, 45067 Orléans, France; (M.-A.H.); (F.S.)
| | - Khaoula Mkhayar
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez 30040, Morocco; (K.M.); (S.E.)
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez 30040, Morocco; (K.M.); (S.E.)
| | - Nabil El Brahmi
- Euromed Research Center, Euromed Faculty of Pharmacy, School of Engineering in Biomedical and Biotechnology, Euromed University of Fes (UEMF), Meknes Road, Fez 30000, Morocco; (A.E.A.); (N.E.B.)
| | - Marie-Aude Hiebel
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, BP 6759, CEDEX 2, 45067 Orléans, France; (M.-A.H.); (F.S.)
| | - Jérôme Bignon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France;
| | - Gérald Guillaumet
- Euromed Research Center, Euromed Faculty of Pharmacy, School of Engineering in Biomedical and Biotechnology, Euromed University of Fes (UEMF), Meknes Road, Fez 30000, Morocco; (A.E.A.); (N.E.B.)
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, BP 6759, CEDEX 2, 45067 Orléans, France; (M.-A.H.); (F.S.)
| | - Franck Suzenet
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, BP 6759, CEDEX 2, 45067 Orléans, France; (M.-A.H.); (F.S.)
| | - Saïd El Kazzouli
- Euromed Research Center, Euromed Faculty of Pharmacy, School of Engineering in Biomedical and Biotechnology, Euromed University of Fes (UEMF), Meknes Road, Fez 30000, Morocco; (A.E.A.); (N.E.B.)
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da Rocha JAP, da Costa RA, da Costa ADSS, da Rocha ECM, Gomes AJB, Machado AK, Fagan SB, Brasil DDSB, Lima e Lima AH. Harnessing Brazilian biodiversity database: identification of flavonoids as potential inhibitors of SARS-CoV-2 main protease using computational approaches and all-atom molecular dynamics simulation. Front Chem 2024; 12:1336001. [PMID: 38456183 PMCID: PMC10917896 DOI: 10.3389/fchem.2024.1336001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the etiological agent responsible for the global outbreak of COVID-19 (Coronavirus Disease 2019). The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a vital role in mediating viral replication and transcription. In this study, a comprehensive computational approach was employed to investigate the binding affinity, selectivity, and stability of natural product candidates as potential new antivirals acting on the viral polyprotein processing mediated by SARS-CoV-2 Mpro. A library of 288 flavonoids extracted from Brazilian biodiversity was screened to select potential Mpro inhibitors. An initial filter based on Lipinski's rule of five was applied, and 204 compounds that did not violate any of the Lipinski rules were selected. The compounds were then docked into the active site of Mpro using the GOLD program, and the poses were subsequently re-scored using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) binding free energy calculations performed by AmberTools23. The top five flavonoids with the best MM-GBSA binding free energy values were selected for analysis of their interactions with the active site residues of the protein. Next, we conducted a toxicity and drug-likeness analysis, and non-toxic compounds were subjected to molecular dynamics simulation and free energy calculation using the MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. It was observed that the five selected flavonoids had lower MM-GBSA binding free energy with Mpro than the co-crystal ligand. Furthermore, these compounds also formed hydrogen bonds with two important residues, Cys145 and Glu166, in the active site of Mpro. Two compounds that passed the drug-likeness filter showed stable conformations during the molecular dynamics simulations. Among these, NuBBE_867 exhibited the best MM-PBSA binding free energy value compared to the crystallographic inhibitor. Therefore, this study suggests that NuBBE_867 could be a potential inhibitor against the main protease of SARS-CoV-2 and may be further examined to confirm our results.
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Affiliation(s)
- João Augusto Pereira da Rocha
- Laboratory of Modeling and Computational Chemistry, Federal Institute of Education, Science and Technology of Paraná (IFPA) Campus Bragança, Bragança, Brazil
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Renato Araújo da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education Science and Technology of Paraná (IFPA) Campus Abaetetuba, Abaetetuba, Brazil
| | - Andreia do Socorro Silva da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Elaine Cristina Medeiros da Rocha
- Laboratory of Modeling and Computational Chemistry, Federal Institute of Education, Science and Technology of Paraná (IFPA) Campus Bragança, Bragança, Brazil
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Anderson José Bahia Gomes
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education Science and Technology of Paraná (IFPA) Campus Abaetetuba, Abaetetuba, Brazil
| | | | | | - Davi do Socorro Barros Brasil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Anderson Henrique Lima e Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
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Bulbule RR, Jadav T, Rajput N, Das R, Chatterjee DR, Shard A, Sengupta P. Comprehensive characterization and preclinical assessment of an imidazopyridine-based anticancer lead molecule. Drug Dev Res 2024; 85:e22139. [PMID: 38084651 DOI: 10.1002/ddr.22139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 02/15/2024]
Abstract
Imidazopyridine scaffold holds significant pharmacological importance in the treatment of cancer. An in-house synthesized imidazopyridine-based molecule was found to have promising anticancer activity against breast cancer, lung cancer, and colon cancer. The molecule is an inhibitor of pyruvate kinase M2, the enzyme that elevates tumor growth, metastasis and chemoresistance by directly controlling tumor cell metabolism. Screening of the physicochemical properties of any lead molecules is essential to avoid failure in late-stage drug development. In this research, the physicochemical properties of the molecule including log P, log D, pKa, and plasma protein binding were assessed to check its drug-likeness. Plasma and metabolic stability of the molecule were also evaluated. Moreover, pharmacokinetic profiles of the lead molecule in Sprague-Dawley rats and in vitro metabolite identification studies were also performed. Finally, an in silico software, Pro-Tox-II, was used to predict toxicity of the molecule and its metabolites. Log P, Log D (pH 7.4), pKa, and plasma protein binding of the molecule were found to be 2.03%, 2.42%, 10.4%, and 98%, respectively. The molecule was stable in plasma and metabolic conditions. A total of nine new metabolites were identified and characterized. Cmax and t½ of this molecule were found to be 4016 ± 313.95 ng/mL and 9.57 ± 3.05 h, respectively. Based on the previously reported study and this finding, the molecule can be considered as a promising anticancer lead with potential drug-likeness properties. Further preclinical and clinical drug discovery studies may be initiated in continuation of this study in search of a potential anticancer lead.
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Affiliation(s)
- Ratik Ramesh Bulbule
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Tarang Jadav
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Niraj Rajput
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Pinaki Sengupta
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
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Ahmed S, Tabish M. Phytocompounds screening of Nigella sativa in terms of human cancer by targeting sphingosine kinase-1 and pyruvate kinase-M2: a study based on in silico analysis. J Biomol Struct Dyn 2024; 42:1544-1558. [PMID: 37194426 DOI: 10.1080/07391102.2023.2212773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/03/2023] [Indexed: 05/18/2023]
Abstract
Cancer is a multifactorial disease that can cause morbidity and mortality in humans. An altered gene expression in cancer leads to a change in the overall activity of the human cell. Overexpression of cancer protein may give a piece of wide information about the specific type of tumor. Sphingosine kinase-1 (SK-1) is a metabolic enzyme that is mainly overexpressed in several types of cancer and other inflammatory diseases. Similarly, pyruvate kinase-M2 (PK-M2) is an important oncogenic ATP-producing glycolytic enzyme that is upregulated in most cancer cells. The phytocompound of medicinal plants such as Nigella sativa contains a variety of micronutrients that inhibit the proliferation and activity of tumor cells. In this study, the role of phytocompounds in combating cancer was studied against the model kinase proteins, that is, PK-M2 and SK-1. In silico tool like the PASS-Way2Drug server was used to predict the anticancer properties of phytocompounds. Moreover, the CLC-Pred web server provided the cytotoxicity prediction of chemical compounds against several human cancer cell lines. The pharmacokinetics and toxicity profiles were predicted by the SwissADME and pkCSM software. The binding energies were obtained by molecular docking to confirm the intermolecular interaction of selected phytocompounds with proteins. Consequently, molecular dynamics (MD) simulation confirmed the stability, conformational changes, and dynamic behavior of the kinase proteins complexed with the lead phytocompounds, that is, epicatechin, apigenin, and kaempferol.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, Uttar Pradesh, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, Uttar Pradesh, India
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Acharya A, Yadav M, Nagpure M, Kumaresan S, Guchhait SK. Molecular medicinal insights into scaffold hopping-based drug discovery success. Drug Discov Today 2024; 29:103845. [PMID: 38013043 DOI: 10.1016/j.drudis.2023.103845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
In both academia and the pharmaceutical industry, innovative hypotheses, methodologies and technologies that can shorten the drug research and development, leading to higher success rates, are vital. In this review, we demonstrate how innovative variations of the scaffold-hopping strategy have been used to create new druggable molecular spaces, drugs, clinical candidates, preclinical candidates, and bioactive agents. We also analyze molecular modulations that enabled improvements of the pharmacodynamic (PD), physiochemical, and pharmacokinetic (PK) properties (P3 properties) of the drugs resulting from these scaffold-hopping strategies.
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Affiliation(s)
- Ayan Acharya
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Mukul Yadav
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Mithilesh Nagpure
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Sanathanalaxmi Kumaresan
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India; National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India
| | - Sankar K Guchhait
- National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab 160062, India.
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Almalki AA, Shafie A, Hazazi A, Banjer HJ, Bakhuraysah MM, Almaghrabi SA, Alsaiari AA, Alsaeedi FA, Ashour AA, Alharthi A, Alharthi NS, Anjum F. Targeting Cathepsin L in Cancer Management: Leveraging Machine Learning, Structure-Based Virtual Screening, and Molecular Dynamics Studies. Int J Mol Sci 2023; 24:17208. [PMID: 38139037 PMCID: PMC10743089 DOI: 10.3390/ijms242417208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Cathepsin L (CTSL) expression is dysregulated in a variety of cancers. Extensive empirical evidence indicates their direct participation in cancer growth, angiogenic processes, metastatic dissemination, and the development of treatment resistance. Currently, no natural CTSL inhibitors are approved for clinical use. Consequently, the development of novel CTSL inhibition strategies is an urgent necessity. In this study, a combined machine learning (ML) and structure-based virtual screening strategy was employed to identify potential natural CTSL inhibitors. The random forest ML model was trained on IC50 values. The accuracy of the trained model was over 90%. Furthermore, we used this ML model to screen the Biopurify and Targetmol natural compound libraries, yielding 149 hits with prediction scores >0.6. These hits were subsequently selected for virtual screening using a structure-based approach, yielding 13 hits with higher binding affinity compared to the positive control (AZ12878478). Two of these hits, ZINC4097985 and ZINC4098355, have been shown to strongly bind CTSL proteins. In addition to drug-like properties, both compounds demonstrated high affinity, ligand efficiency, and specificity for the CTSL binding pocket. Furthermore, in molecular dynamics simulations spanning 200 ns, these compounds formed stable protein-ligand complexes. ZINC4097985 and ZINC4098355 can be considered promising candidates for CTSL inhibition after experimental validation, with the potential to provide therapeutic benefits in cancer management.
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Affiliation(s)
- Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia;
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Maha M. Bakhuraysah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Sarah Abdullah Almaghrabi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Center of Innovations in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Fouzeyyah Ali Alsaeedi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif 21944, Saudi Arabia;
| | - Afaf Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Nahed S. Alharthi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
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9
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Zhou Y, He Y, Teng X, Mi J, Yang J, Wei R, Liu W, Ma Q, Tan Z, Sang Z. Development of novel salicylic acid-donepezil-rivastigmine hybrids as multifunctional agents for the treatment of Alzheimer's disease. J Enzyme Inhib Med Chem 2023; 38:2231661. [PMID: 37414563 DOI: 10.1080/14756366.2023.2231661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 07/08/2023] Open
Abstract
Alzheimer's disease (AD) is a chronic, progressive brain degenerative disease that is common in the elderly. So far, there is no effective treatment. The multi-target-directed ligands (MTDLs) strategy has been recognised as the most promising approach due to the complexity of the pathogenesis of AD. Herein, novel salicylic acid-donepezil-rivastigmine hybrids were designed and synthesised. The bioactivity results exhibited that 5a was a reversible and selective eqBChE inhibitor (IC50 = 0.53 μM), and the docking provided the possible mechanism. Compound 5a also displayed potential anti-inflammatory effects and significant neuroprotective effect. Moreover, 5a exhibited favourable stabilities in artificial gastrointestinal solution and plasma. Finally, 5a demonstrated potential cognitive improvement in scopolamine-induced cognitive dysfunction. Hence, 5a was a potential multifunctional lead compound against AD.
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Affiliation(s)
- Yi Zhou
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Ying He
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Xue Teng
- Key Laboratory of Tropical Biological Resources of Ministry of Education and One Health Institute, School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Jing Mi
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Jing Yang
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Rongrui Wei
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine of Ministry of Education, Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Wenmin Liu
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
| | - Qinge Ma
- Key Laboratory of Modern Preparation of Traditional Chinese Medicine of Ministry of Education, Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Zhenghuai Tan
- Institute of Traditional Chinese Medicine Pharmacology and Toxicology, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Zhipei Sang
- College of Chemistry and Pharmaceutical Engineering, Nanyang Normal University, Nanyang, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education and One Health Institute, School of Pharmaceutical Sciences, Hainan University, Haikou, China
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10
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Sasaki T, Kasama T, Nokihara K. A novel cyclic peptide library immobilized on gel-type beads focusing on rapid construction and characterization for comprehensive drug discovery. Chem Biol Drug Des 2023; 102:1327-1335. [PMID: 37658589 DOI: 10.1111/cbdd.14331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Medium sized molecules such as peptides and macrocycles have recently drawn much attention as potent sources of medicinal lead compounds, whereas the possibility of obtaining a practical drug from them remains limited. The present paper describes a concept of discovering novel medicinal targets or binding modes as well as lead compounds by the one-peptide-on-one-bead (OPOB) technology for comprehensive screening. The difficulty and problems in conventional drug discovery methods that generally deal with one predetermined target are considered. The building blocks used for the present libraries were selected based on previous results in development of peptidic drugs. Each constituent has the common structure of cyclic form prepared by disulfide of cysteinyl residues or thioether linkages, additionally a methionine residue was inserted for the site-specific rapid cleavage by cyanogen bromide to liberate the immobilized peptides allowing reliable characterization by MALDI-TOF-MS/MS without LC-purification. Thus, a high throughput construction method for cyclic peptide libraries as well as characterization of single bead are proposed for drug discovery.
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11
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Riaz F, Hossain MS, Roney M, Ali Y, Qureshi S, Muhammad R, Moshawih S, Abd Hamid S, Seidel V, Ur Rashid H, Ming LC. Evaluation of potential bacterial protease inhibitor properties of selected hydroxyquinoline derivatives: an in silico docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2023; 41:9756-9769. [PMID: 36399018 DOI: 10.1080/07391102.2022.2146200] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/06/2022] [Indexed: 11/21/2022]
Abstract
Antimicrobial drug resistance (AMR) is a severe global threat to public health. The increasing emergence of drug-resistant bacteria requires the discovery of novel antibacterial agents. Quinoline derivatives have previously been reported to exhibit antimalarial, antiviral, antitumor, antiulcer, antioxidant and, most interestingly, antibacterial properties. In this study, we evaluated the binding affinity of three newly designed hydroxyquinolines derived from sulfanilamide (1), 4-amino benzoic acid (2) and sulfanilic acid (3) towards five bacterial protein targets (PDB ID: 1JIJ, 3VOB, 1ZI0, 6F86, 4CJN). The three derivatives were designed considering the amino acid residues identified at the active site of each protein involved in the binding of each co-crystallized ligand and drug-likeness properties. The ligands displayed binding energy values with the target proteins ranging from -2.17 to -8.45 kcal/mol. Compounds (1) and (3) showed the best binding scores towards 1ZI0/3VOB and 1JIJ/4CJN, respectively, which may serve as new antibiotic scaffolds. Our in silico results suggest that sulfanilamide (1) or sulfanilic acid (3) hydroxyquinoline derivatives have the potential to be developed as bacterial inhibitors, particularly MRSA inhibitors. But before that, it must go through the proper preclinical and clinical trials for further scientific validation. Further experimental studies are warranted to explore the antibacterial potential of these compounds through preclinical and clinical studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faiza Riaz
- Department of Chemistry, Sarhad University of Science and Information Technology, Peshawar, Pakistan
| | - Md Sanower Hossain
- Centre for Sustainability of Ecosystem and Earth Resources (Pusat ALAM), Universiti Malaysia Pahang, Kuantan, Malaysia
| | - Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang,Kuantan, Pahang Darul Makmur, Malaysia
| | - Yousaf Ali
- Faculty of Allied Health Sciences, Iqra National University Swat Campus, Khyber Pakhtunkhwa, Pakistan
| | - Saira Qureshi
- Department of Chemistry, Sarhad University of Science and Information Technology, Peshawar, Pakistan
| | - Riaz Muhammad
- Department of Chemistry, Sarhad University of Science and Information Technology, Peshawar, Pakistan
| | - Said Moshawih
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Shafida Abd Hamid
- Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Veronique Seidel
- Natural Products Research Laboratory, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Haroon Ur Rashid
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Long Chiau Ming
- PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
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12
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Caminero Gomes Soares A, Marques Sousa GH, Calil RL, Goulart Trossini GH. Absorption matters: A closer look at popular oral bioavailability rules for drug approvals. Mol Inform 2023; 42:e202300115. [PMID: 37550251 DOI: 10.1002/minf.202300115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/10/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
This study examines how two popular drug-likeness concepts used in early development, Lipinski Rule of Five (Ro5) and Veber's Rules, possibly affected drug profiles of FDA approved drugs since 1997. Our findings suggest that when all criteria are applied, relevant compounds may be excluded, addressing the harmfulness of blindly employing these rules. Of all oral drugs in the period used for this analysis, around 66 % conform to the RO5 and 85 % to Veber's Rules. Molecular Weight and calculated LogP showed low consistent values over time, apart from being the two least followed rules, challenging their relevance. On the other hand, hydrogen bond related rules and the number of rotatable bonds are amongst the most followed criteria and show exceptional consistency over time. Furthermore, our analysis indicates that topological polar surface area and total count of hydrogen bonds cannot be used as interchangeable parameters, contrary to the original proposal. This research enhances the comprehension of drug profiles that were FDA approved in the post-Lipinski period. Medicinal chemists could utilize these heuristics as a limited guide to direct their exploration of the oral bioavailability chemical space, but they must also steer the wheel to break these rules and explore different regions when necessary.
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Affiliation(s)
- Artur Caminero Gomes Soares
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Laboratório de Integração entre Técnicas Experimentais e Computacionais (LITEC), Av. Prof. Lineu Prestes, 580, São Paulo, SP, Brazil
| | - Gustavo Henrique Marques Sousa
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Laboratório de Integração entre Técnicas Experimentais e Computacionais (LITEC), Av. Prof. Lineu Prestes, 580, São Paulo, SP, Brazil
| | - Raisa Ludmila Calil
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Laboratório de Integração entre Técnicas Experimentais e Computacionais (LITEC), Av. Prof. Lineu Prestes, 580, São Paulo, SP, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Laboratório de Integração entre Técnicas Experimentais e Computacionais (LITEC), Av. Prof. Lineu Prestes, 580, São Paulo, SP, Brazil
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13
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Flores R, Iqbal S, Sikazwe D. Phenylacetyl-/Trolox- Amides: Synthesis, Sigma-1, HDAC-6, and Antioxidant Activities. Int J Mol Sci 2023; 24:15295. [PMID: 37894975 PMCID: PMC10607876 DOI: 10.3390/ijms242015295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/07/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
In search of novel multi-mechanistic approaches for treating Alzheimer's disease (AD), we have embarked on synthesizing single small molecules for probing contributory roles of the following combined disease targets: sigma-1 (σ-1), class IIb histone deacetylase-6 (HDAC-6), and oxidative stress (OS). Herein, we report the synthesis and partial evaluation of 20 amides (i.e., phenylacetic and Trolox or 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid derivatives). Target compounds were conveniently synthesized via amidation by either directly reacting acyl chlorides with amines or condensing acids with amines in the presence of coupling agents 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo [4,5-b] pyridinium 3-oxide hexafluorophosphate (HATU) or 1,1'-carbonyldiimidazole (CDI). Overall, this project afforded compound 8 as a promising lead with σ-1 affinity (Ki = 2.1 μM), HDAC-6 (IC50 = 17 nM), and antioxidant (1.92 Trolox antioxidant equivalents or TEs) activities for optimization in ensuing structure-activity relationship (SAR) studies.
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Affiliation(s)
| | | | - Donald Sikazwe
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA; (R.F.); (S.I.)
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14
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Zhang C, Sui Y, Liu S, Yang M. Anti-Viral Activity of Bioactive Molecules of Silymarin against COVID-19 via In Silico Studies. Pharmaceuticals (Basel) 2023; 16:1479. [PMID: 37895950 PMCID: PMC10610370 DOI: 10.3390/ph16101479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection drove the global coronavirus disease 2019 (COVID-19) pandemic, causing a huge loss of human life and a negative impact on economic development. It is an urgent necessity to explore potential drugs against viruses, such as SARS-CoV-2. Silymarin, a mixture of herb-derived polyphenolic flavonoids extracted from the milk thistle, possesses potent antioxidative, anti-apoptotic, and anti-inflammatory properties. Accumulating research studies have demonstrated the killing activity of silymarin against viruses, such as dengue virus, chikungunya virus, and hepatitis C virus. However, the anti-COVID-19 mechanisms of silymarin remain unclear. In this study, multiple disciplinary approaches and methodologies were applied to evaluate the potential mechanisms of silymarin as an anti-viral agent against SARS-CoV-2 infection. In silico approaches such as molecular docking, network pharmacology, and bioinformatic methods were incorporated to assess the ligand-protein binding properties and analyze the protein-protein interaction network. The DAVID database was used to analyze gene functions, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment. TCMSP and GeneCards were used to identify drug target genes and COVID-19-related genes. Our results revealed that silymarin compounds, such as silybin A/B and silymonin, displayed triplicate functions against SARS-CoV-2 infection, including directly binding with human angiotensin-converting enzyme 2 (ACE2) to inhibit SARS-CoV-2 entry into the host cells, directly binding with viral proteins RdRp and helicase to inhibit viral replication and proliferation, and regulating host immune response to indirectly inhibit viral infection. Specifically, the targets of silymarin molecules in immune regulation were screened out, such as proinflammatory cytokines TNF and IL-6 and cell growth factors VEGFA and EGF. In addition, the molecular mechanism of drug-target protein interaction was investigated, including the binding pockets of drug molecules in human ACE2 and viral proteins, the formation of hydrogen bonds, hydrophobic interactions, and other drug-protein ligand interactions. Finally, the drug-likeness results of candidate molecules passed the criteria for drug screening. Overall, this study demonstrates the molecular mechanism of silymarin molecules against SARS-CoV-2 infection.
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Affiliation(s)
- Chunye Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA;
| | - Yuxiang Sui
- School of Life Science, Shanxi Normal University, Linfen 041004, China;
| | - Shuai Liu
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310006, China;
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO 65212, USA
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA
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15
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Algethami FK, Jlizi S, Znati M, Elamin MR, Ben Hamadi N, Ben Jannet H. Chemical composition, antioxidant and anti-tyrosinase potentials of Acacia cyclops trunk bark using in vitro and in silico approaches. Nat Prod Res 2023:1-12. [PMID: 37812151 DOI: 10.1080/14786419.2023.2266103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
The purpose of this paper was to evaluate the phytochemical profile of Acacia cyclops trunk bark methanol extract using LC-MS/MS, as well as to assess its antioxidant and anti-tyrosinase activities. Thus, total phenolic and flavonoid contents of the studied extract were established and 19 compounds were detected and quantified. In addition of their antioxidant potential against DPPH and ABTS assays, in vitro and in silico studies were adopted to evaluate tyrosinase inhibitory property of A. cyclops extract. Methanol trunk bark extract showed significant total phenolic content, antioxidant potential in terms of free radical scavenging, as well as an interesting tyrosinase inhibitory action (IC50= 05.12 ± 0.41 μg/mL). The molecular docking analysis and the drug-likeness prediction of the major selected compounds supported the significant anti-tyrosinase activity of the studied extract. The obtained results suggest that A. cyclops extract could be a promising candidate in the treatment of skin hyperpigmentation disorders.
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Affiliation(s)
- Faisal K Algethami
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Salma Jlizi
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Team: Medicinal Chemistry and Natural Products, Faculty of Science of Monastir, University of Monastir, Monastir, Tunisia
| | - Mansour Znati
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Team: Medicinal Chemistry and Natural Products, Faculty of Science of Monastir, University of Monastir, Monastir, Tunisia
| | - Mohamed R Elamin
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Naoufel Ben Hamadi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Team: Medicinal Chemistry and Natural Products, Faculty of Science of Monastir, University of Monastir, Monastir, Tunisia
| | - Hichem Ben Jannet
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Team: Medicinal Chemistry and Natural Products, Faculty of Science of Monastir, University of Monastir, Monastir, Tunisia
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Ahmed S, Mahendiran D, Bhat AR, Rahiman AK. Theoretical, in Vitro Antiproliferative, and in Silico Molecular Docking and Pharmacokinetics Studies of Heteroleptic Nickel(II) and Copper(II) Complexes of Thiosemicarbazone-Based Ligands and Pefloxacin. Chem Biodivers 2023; 20:e202300702. [PMID: 37528701 DOI: 10.1002/cbdv.202300702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023]
Abstract
Twelve new heteroleptic nickel(II) and copper(II) complexes of the type [M(L1-6 )(Pfx)2 ] (1-12), where L1-6 =2-benzylidenehydrazinecarbothioamide (L1 ), 2-benzylidene-N-methylhydrazinecarbothioamide (L2 ), 2-benzylidene-N-phenylhydrazinecarbothioamide (L3 ), 2-(4-methylbenzylidene)hydrazinecarbothioamide (L4 ), 2-(4-methylbenzylidene)-N-methylhydrazinecarbothioamide (L5 ) and 2-(4-methylbenzylidene)-N-phenylhydrazinecarbothioamide (L6 ), Pfx=pefloxacin and M=Ni(II) or Cu(II) have been synthesised, and their structures were confirmed by different spectral techniques. The spectral data and density functional theory (DFT) calculations supported the bonding of pefloxacin drug molecule via one of the carboxylate oxygen atoms and the pyridone oxygen atom, and the thiosemicarbazone ligand via the imine nitrogen and the thione sulfur atoms with the metal(II) ion, forming distorted octahedral geometry. In vitro antiproliferative activity of the synthesized complexes was evaluated against three human breast cancer (T47D, estrogen negative (MDA-MB-231) and estrogen positive (MCF-7)) as well as non-tumorigenic human breast epithelial (MCF-10a) cell lines, which showed the higher activity for the copper(II) complexes. The interaction of the synthesized complexes with an oncogenic protein H-ras (121 p) was explored by in silico molecular docking studies. Further, in silico pharmacokinetics and ADMET parameters were also analysed to predict the drug-likeness as well as non-toxic and non-carcinogenic behavior, and safe oral administration of the complexes.
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Affiliation(s)
- Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, 600 014, India
| | - Dharmasivam Mahendiran
- Center for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, 4111, Australia
| | - Ajmal Rashid Bhat
- Department of Chemistry, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, 440 033, India
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, 600 014, India
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17
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Gheidari D, Mehrdad M, Bayat M. Novel indenopyrrol-4-one derivatives as potent BRDT inhibitors: synthesis, molecular docking, drug-likeness, ADMET, and DFT studies. J Biomol Struct Dyn 2023:1-14. [PMID: 37528682 DOI: 10.1080/07391102.2023.2242502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/23/2023] [Indexed: 08/03/2023]
Abstract
We synthesized new, structurally distinct series of indeno[1,2-b]pyrrol-4(1H)-ones. Effective derivatives were found by in silico screening, and our studies revealed that compound 5h exhibited good binding energies for inhibition of BRDT. In addition, DFT studies were carried out by means of the B3LYP/6-3lG basis set in the gas phase to investigate the conformation of protein-ligand interactions. The results of the investigation suggest that these compounds could be considered novel BRDT inhibitors. The pharmacokinetic and drug-like properties of the new indenopyrrol-4(1H)-one derivatives exhibited that these compounds could be represented as potential candidates for further development into anticancer-like agents. Additionally, based on the optimised structures, the optimum geometry for each of the selected molecules was developed. Then, the estimated and the experimentally determined IR vibrational frequencies for each compound were compared. The results of this comparison showed that the theoretical and experimental data were in excellent agreement, which could support the reliability of the experimental analytical data and the applicability of the mathematical model.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Davood Gheidari
- Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran
| | - Morteza Mehrdad
- Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran
| | - Mohammad Bayat
- Department of Chemistry, Faculty of Science, Imam Khomeini International University, Qazvin, Iran
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Akash S, Mir SA, Mahmood S, Hossain S, Islam MR, Mukerjee N, Nayak B, Nafidi HA, Bin Jardan YA, Mekonnen A, Bourhia M. Novel computational and drug design strategies for inhibition of monkeypox virus and Babesia microti: molecular docking, molecular dynamic simulation and drug design approach by natural compounds. Front Microbiol 2023; 14:1206816. [PMID: 37538847 PMCID: PMC10394520 DOI: 10.3389/fmicb.2023.1206816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/20/2023] [Indexed: 08/05/2023] Open
Abstract
Background The alarming increase in tick-borne pathogens such as human Babesia microti is an existential threat to global public health. It is a protozoan parasitic infection transmitted by numerous species of the genus Babesia. Second, monkeypox has recently emerged as a public health crisis, and the virus has spread around the world in the post-COVID-19 period with a very rapid transmission rate. These two novel pathogens are a new concern for human health globally and have become a significant obstacle to the development of modern medicine and the economy of the whole world. Currently, there are no approved drugs for the treatment of this disease. So, this research gap encourages us to find a potential inhibitor from a natural source. Methods and materials In this study, a series of natural plant-based biomolecules were subjected to in-depth computational investigation to find the most potent inhibitors targeting major pathogenic proteins responsible for the diseases caused by these two pathogens. Results Among them, most of the selected natural compounds are predicted to bind tightly to the targeted proteins that are crucial for the replication of these novel pathogens. Moreover, all the molecules have outstanding ADMET properties such as high aqueous solubility, a higher human gastrointestinal absorption rate, and a lack of any carcinogenic or hepatotoxic effects; most of them followed Lipinski's rule. Finally, the stability of the compounds was determined by molecular dynamics simulations (MDs) for 100 ns. During MDs, we observed that the mentioned compounds have exceptional stability against selected pathogens. Conclusion These advanced computational strategies reported that 11 lead compounds, including dieckol and amentoflavone, exhibited high potency, excellent drug-like properties, and no toxicity. These compounds demonstrated strong binding affinities to the target enzymes, especially dieckol, which displayed superior stability during molecular dynamics simulations. The MM/PBSA method confirmed the favorable binding energies of amentoflavone and dieckol. However, further in vitro and in vivo studies are necessary to validate their efficacy. Our research highlights the role of Dieckol and Amentoflavone as promising candidates for inhibiting both monkeypox and Babesia microti, demonstrating their multifaceted roles in the control of these pathogens.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Showkat Ahmad Mir
- School of Life Sciences, Sambalpur University, Sambalpur, Odisha, India
| | - Sajjat Mahmood
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Saddam Hossain
- Department of Biomedical Engineering, Faculty of Engineering and Technology, Islamic University, Kushtia, Bangladesh
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Sambalpur, Odisha, India
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amare Mekonnen
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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19
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Moawadh MS. Molecular docking analysis of natural compounds as TNF-α inhibitors for Crohn's disease management. Bioinformation 2023; 19:716-720. [PMID: 37885792 PMCID: PMC10598355 DOI: 10.6026/97320630019716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 10/28/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease that is immune-mediated and affects the gastrointestinal tract. The chronic and severe nature of this condition leads to diminished health-related life quality, and frequent hospitalization. While medications such as sulfasalazine, corticosteroids, and immuno-suppressants are used to manage the condition, there are no definite treatments for pain and inflammation associated with CD. TNF-α is a prominent target, and medicines such as infliximab and adalimumab have pharmacological efficacy; however, they also have significant toxicity. Here, the natural compound library (2706 compounds) was screened against TNF-α to find natural TNF-α inhibitors to combat CD. The compounds namely ZINC5223934, ZINC6482465, ZINC4098633, ZINC1702729, and ZINC4649679 had higher binding affinity and interaction with the TNF-α protein than the positive control. Furthermore, these compounds had promising drug-like properties, indicating their potential for future exploration and optimization as TNF-α inhibitors for the treatment of CD.
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Affiliation(s)
- Mamdoh S Moawadh
- />Medical Technology Department, Faculty of Applied Medical Sciences, University of Tabuk, Saudi Arabia
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20
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Akash S, Bayıl I, Rahman MA, Mukerjee N, Maitra S, Islam MR, Rajkhowa S, Ghosh A, Al-Hussain SA, Zaki MEA, Jaiswal V, Sah S, Barboza JJ, Sah R. Target specific inhibition of West Nile virus envelope glycoprotein and methyltransferase using phytocompounds: an in silico strategy leveraging molecular docking and dynamics simulation. Front Microbiol 2023; 14:1189786. [PMID: 37455711 PMCID: PMC10338848 DOI: 10.3389/fmicb.2023.1189786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023] Open
Abstract
Mosquitoes are the primary vector for West Nile virus, a flavivirus. The virus's ability to infiltrate and establish itself in increasing numbers of nations has made it a persistent threat to public health worldwide. Despite the widespread occurrence of this potentially fatal disease, no effective treatment options are currently on the market. As a result, there is an immediate need for the research and development of novel pharmaceuticals. To begin, molecular docking was performed on two possible West Nile virus target proteins using a panel of twelve natural chemicals, including Apigenin, Resveratrol, Hesperetin, Fungisterol, Lucidone, Ganoderic acid, Curcumin, Kaempferol, Cholic acid, Chlorogenic acid, Pinocembrin, and Sanguinarine. West Nile virus methyltransferase (PDB ID: 2OY0) binding affinities varied from -7.4 to -8.3 kcal/mol, whereas West Nile virus envelope glycoprotein affinities ranged from -6.2 to -8.1 kcal/mol (PDB ID: 2I69). Second, substances with larger molecular weights are less likely to be unhappy with the Lipinski rule. Hence, additional research was carried out without regard to molecular weight. In addition, compounds 01, 02, 03, 05, 06, 07, 08, 09, 10 and 11 are more soluble in water than compound 04 is. Besides, based on maximum binding affinity, best three compounds (Apigenin, Curcumin, and Ganoderic Acid) has been carried out molecular dynamic simulation (MDs) at 100 ns to determine their stability. The MDs data is also reported that these mentioned molecules are highly stable. Finally, advanced principal component analysis (PCA), dynamics cross-correlation matrices (DCCM) analysis, binding free energy and dynamic cross correlation matrix (DCCM) theoretical study is also included to established mentioned phytochemical as a potential drug candidate. Research has indicated that the aforementioned natural substances may be an effective tool in the battle against the dangerous West Nile virus. This study aims to locate a bioactive natural component that might be used as a pharmaceutical.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Türkiye
| | | | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Swastika Maitra
- Department of Microbiology, Adamas University, Kolkata, West Bengal, India
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Gwahati, Assam, India
| | - Sami A. Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Vikash Jaiswal
- Department of Cardiovascular Research, Larkin Community Hospital, South Miami, FL, United States
| | - Sanjit Sah
- Global Consortium for Public Health and Research, Datta Meghe Institute of Higher Education and Research, Jawaharlal Nehru Medical College, Wardha, India
- SR Sanjeevani Hospital, Kayanpur, Siraha, Nepal
| | | | - Ranjit Sah
- Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
- Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
- Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
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21
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Anichina K, Georgiev N, Lumov N, Vuchev D, Popova-Daskalova G, Momekov G, Cherneva E, Mihaylova R, Mavrova A, Atanasova-Vladimirova S, Piroeva I, Yancheva D. Fused Triazinobenzimidazoles Bearing Heterocyclic Moiety: Synthesis, Structure Investigations, and In Silico and In Vitro Biological Activity. Molecules 2023; 28:5034. [PMID: 37446695 DOI: 10.3390/molecules28135034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
[1,3,5]Triazino[1,2-a]benzimidazole-2-amines bearing heterocyclic moiety in 4-position were synthesized. The compounds were characterized by elemental analysis, IR, 1H-NMR, 13C-NMR, and HRMS spectroscopy. The molecular geometry and electron structure of these molecules were theoretically studied using density functional theory (DFT) methods. The molecular structure of the synthesized fused triazinobenzimidazole was confirmed to correspond to the 3,4-dihydrotriazinobenzimidazole structure through the analysis of spectroscopic NMR data and DFT calculations. The antinematodic activity was evaluated in vitro on isolated encapsulated muscle larvae (ML) of Trichinella spiralis. The results showed that the tested triazinobenzimidazoles exhibit significantly higher efficiency than the conventional drug used to treat trichinosis, albendazole, at a concentration of 50 μg/mL. The compound 3c substituted with a thiophen-2-yl moiety exhibited the highest anthelmintic activity, with a larvicidal effect of 58.41% at a concentration of 50 μg/mL after 24 h of incubation. Following closely behind, the pyrrole analog 3f demonstrated 49.90% effectiveness at the same concentration. The preliminary structure-anti-T. spiralis activity relationship (SAR) of the analogues in the series was discussed. The cytotoxicity of the benzimidazole derivatives against two normal fibroblast cells (3T3 and CCL-1) and two cancer human cell lines (MCF-7 breast cancer cells and chronic myeloid leukemia cells AR-230) was evaluated using the MTT-dye reduction assay. The screening results indicated that the compounds showed no cytotoxicity against the tested cell lines. An in silico study of the physicochemical and pharmacokinetic characteristics of the novel synthesized fused triazinobenzimidazoles showed that they were characterized by a significant degree of drug-likeness and optimal properties for anthelmintic agents.
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Affiliation(s)
- Kameliya Anichina
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridski Blvd., 1756 Sofia, Bulgaria
| | - Nikolai Georgiev
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridski Blvd., 1756 Sofia, Bulgaria
| | - Nikolay Lumov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 9, 1113 Sofia, Bulgaria
| | - Dimitar Vuchev
- Department of Infectious Diseases, Parasitology and Tropical Medicine, Medical University, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Galya Popova-Daskalova
- Department of Infectious Diseases, Parasitology and Tropical Medicine, Medical University, 15A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Georgi Momekov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Emiliya Cherneva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 9, 1113 Sofia, Bulgaria
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Rositsa Mihaylova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Anelia Mavrova
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridski Blvd., 1756 Sofia, Bulgaria
| | | | - Iskra Piroeva
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Build. 11, 1113 Sofia, Bulgaria
| | - Denitsa Yancheva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 9, 1113 Sofia, Bulgaria
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22
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Khedkar HN, Chen LC, Kuo YC, Wu ATH, Huang HS. Multi-Omics Identification of Genetic Alterations in Head and Neck Squamous Cell Carcinoma and Therapeutic Efficacy of HNC018 as a Novel Multi-Target Agent for c-MET/STAT3/AKT Signaling Axis. Int J Mol Sci 2023; 24:10247. [PMID: 37373393 DOI: 10.3390/ijms241210247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Amongst the most prevalent malignancies worldwide, head and neck squamous cell carcinoma (HNSCC) is characterized by high morbidity and mortality. The failure of standard treatment modalities, such as surgery, radiotherapy, and chemotherapy, demands the need for in-depth understanding of the complex signaling networks involved in the development of treatment resistance. A tumor's invasive growth and high levels of intrinsic or acquired treatment resistance are the primary causes of treatment failure. This may be a result of the presence of HNSCC's cancer stem cells, which are known to have self-renewing capabilities that result in therapeutic resistance. Using bioinformatics methods, we discovered that elevated expressions of MET, STAT3, and AKT were associated with poor overall survival in HNSCC patients. We then evaluated the therapeutic potential of our newly synthesized small molecule HNC018 towards its potential as a novel anticancer drug. Our computer-aided structure characterization and target identification study predicted that HNC018 could target these oncogenic markers implicated in HNSCC. Subsequently, the HNC018 has demonstrated its anti-proliferative and anticancer activities towards the head and neck squamous cell carcinoma cell lines, along with displaying the stronger binding affinities towards the MET, STAT3, and AKT than the standard drug cisplatin. Reduction in the clonogenic and tumor-sphere-forming ability displays HNC018's role in decreasing the tumorigenicity. Importantly, an vivo study has shown a significant delay in tumor growth in HNC018 alone or in combination with cisplatin-treated xenograft mice model. Collectively with our findings, HNC018 highlights the desirable properties of a drug-like candidate and could be considered as a novel small molecule for treating head and neck squamous cell carcinoma.
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Affiliation(s)
- Harshita Nivrutti Khedkar
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, and Academia Sinica, Taipei 11031, Taiwan
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Lung-Ching Chen
- Division of Cardiology, Department of Internal Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei 11101, Taiwan
- School of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan
| | - Yu-Cheng Kuo
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- School of Post-Baccalaureate Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| | - Alexander T H Wu
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Taipei Heart Institute (THI), Taipei Medical University, Taipei 11031, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Centre, Taipei 11490, Taiwan
| | - Hsu-Shan Huang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, and Academia Sinica, Taipei 11031, Taiwan
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Centre, Taipei 11490, Taiwan
- School of Pharmacy, National Defense Medical Centre, Taipei 11490, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
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23
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Hakeem IJ. Molecular docking analysis of acetylcholinesterase inhibitors for Alzheimer's disease management. Bioinformation 2023; 19:565-570. [PMID: 37886145 PMCID: PMC10599677 DOI: 10.6026/97320630019565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 10/28/2023] Open
Abstract
Alzheimer's disease (AD) is a neurological disease that is related to aging and is the leading cause of dementia globally. AD has a significant influence on cognitive functions, particularly memory, resulting in a variety of functional deficits. Given the increasing prevalence of AD, there is an urgent need for the development of effective therapeutic therapies. In a quest to uncover a holistic remedy for AD, a total of 41 bioactive compounds derived from three distinct medicinal plant sources were screened to evaluate their potential to inhibit the active sites of acetylcholinesterase (AChE). The insilico screening protocol included 24 licorice-derived compounds, 5 ginkgo biloba-derived compounds, and 11 ginseng-derived compounds. Two compounds (Ginkgolide A and Licorice glycoside D2) were observed to display greater binding energy (BE) relative to the control by interacting with crucial residues in the active site of AChE. Ginkgolide A and Licorice glycoside D2 exhibited BEs of -11.3 and -11.2 kcal/mol, respectively, whereas the control, Donepezil, demonstrated a BE of -10.8 kcal/mol. Further, these compounds exhibit favorable drug-likeness properties. This study suggests that further experimental investigations can be conducted on Ginkgolide A and Licorice glycoside D2 to explore their potential therapeutic applications for AD.
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Affiliation(s)
- Israa J Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
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24
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Hua L, Anjum F, Shafie A, Ashour AA, Almalki AA, Alqarni AA, Banjer HJ, Almaghrabi SA, He S, Xu N. Identifying promising GSK3β inhibitors for cancer management: a computational pipeline combining virtual screening and molecular dynamics simulations. Front Chem 2023; 11:1200490. [PMID: 37284581 PMCID: PMC10239944 DOI: 10.3389/fchem.2023.1200490] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/05/2023] [Indexed: 06/08/2023] Open
Abstract
Glycogen synthase kinase-3 (GSK3β), a serine/threonine protein kinase, has been discovered as a novel target for anticancer drugs. Although GSK3β is involved in multiple pathways linked to the etiology of various cancers, no specific GSK3β inhibitor has been authorized for cancer therapy. Most of its inhibitors have toxicity effects therefore, there is a need to develop safe and more potent inhibitors. In this study, a library of 4,222 anti-cancer compounds underwent rigorous computational screening to identify potential candidates for targeting the binding pocket of GSK3β. The screening process involved various stages, including docking-based virtual screening, physicochemical and ADMET analysis, and molecular dynamics simulations. Ultimately, two hit compounds, BMS-754807 and GSK429286A, were identified as having high binding affinities to GSK3β. BMS-754807 and GSK429286A exhibited binding affinities of -11.9, and -9.8 kcal/mol, respectively, which were greater than that of the positive control (-7.6 kcal/mol). Further, molecular dynamics simulations for 100 ns were employed to optimize the interaction between the compounds and GSK3β, and the simulations demonstrated that the interaction was stable and consistent throughout the study. These hits were also anticipated to have good drug-like properties. Finally, this study suggests that BMS-754807 and GSK429286A may undergo experimental validation to evaluate their potential as cancer treatments in clinical settings.
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Affiliation(s)
- Libo Hua
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Saudi Arabia
| | - Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Ali Abdullah Alqarni
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Saudi Arabia
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Sarah Abdullah Almaghrabi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center for Innovations in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shan He
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
- Institute for Nano Scale and Technology, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
- College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, NT, Australia
| | - Nenggui Xu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acupuncture Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
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25
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Krancewicz K, Nowicka-Bauer K, Fiedorowicz K, Marciniak B, Taras-Goslinska K. Thiopurines Analogues with Additional Ring: Synthesis, Spectroscopic Properties, and Anticancer Potency. Int J Mol Sci 2023; 24:ijms24108990. [PMID: 37240336 DOI: 10.3390/ijms24108990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Purine scaffolds constitute a starting point for the synthesis of numerous chemotherapeutics used in treating cancer, viruses, parasites, as well as bacterial and fungal infections. In this work, we synthesized a group of guanosine analogues containing an additional five-membered ring and a sulfur atom at the C-9 position. The spectral, photophysical, and biological properties of the synthesized compounds were investigated. The spectroscopic studies revealed that a combination of the thiocarbonyl chromophore and the tricyclic structure of guanine analogues shifts the absorption region above 350 nm, allowing for selective excitation when present in biological systems. Unfortunately, due to the low fluorescence quantum yield, this process cannot be used to monitor the presence of these compounds in cells. The synthesized compounds were evaluated for their effect on the viability of human cervical carcinoma (HeLa) and mouse fibroblast (NIH/3T3) cells. It was found that all of them display anticancer activity. In vitro studies were preceded by in silico ADME and PASS analyses, which confirmed that the designed compounds are promising candidates for anticancer agents.
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Affiliation(s)
- Katarzyna Krancewicz
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland
| | - Karolina Nowicka-Bauer
- Centre for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznan, Poland
| | - Katarzyna Fiedorowicz
- Nanobiomedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland
| | - Bronislaw Marciniak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland
- Centre for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznan, Poland
| | - Katarzyna Taras-Goslinska
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland
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26
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Lala M, Bhattacharjee S, Ghosh C, Sen A, Sarkar I. In-silico studies on wild orange ( Citrus macroptera Mont.) compounds against COVID-19 pro-inflammation targets. J Biomol Struct Dyn 2023; 41:3511-3523. [PMID: 35297321 DOI: 10.1080/07391102.2022.2051744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 03/05/2022] [Indexed: 12/14/2022]
Abstract
One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however, the specific causes remain unclear. Despite numerous papers that have been flooded in different scientific journals clear clinical picture of COVID-19 aftermath persists to remain fuzzy. The survivors of severe COVID-19infection having defeated the virus are just the starting of an uncharted recovery path. Currently, there is no drug available that is safe to consume to combat this pandemic. However, researchers still struggling to find specific therapeutic solutions. The present study employed an in silico approach to assessing the inhibitory potential of the phytochemicals obtained from GC-MS analysis of Citrus macroptera against inflammatory proteins like COX-2, NMDAR and VCAM-1 which remains in a hyperactive state even after a patient is fully cured of this deadly mRNA virus. An extensive molecular docking investigation of the phyto-compounds at the active binding pockets of the inflammatory proteins revealed the promising inhibitory potential of the phytochemicals. Reasonable physicochemical attributes of the compounds following Lipinski's rule of five, VEBER and PAINS analysis further established them as potential therapeutic candidates against aforesaid inflammatory proteins. MM-GBSA binding free energy estimation revealed that Limonene was the most promising candidate displaying the highest binding efficacy with the concerned VCAM-1 protein included in the present analysis. An interesting finding is the phytochemicals exhibited better binding energy scores with the concerned COX-2, VCAM-1 and NMDA receptor proteins than the conventional drugs that are specifically targeted against them. Our in silico results suggest that all the natural phyto-compounds derived from C. macroptera could be employed in Post covid inflammation complexities after appropriate pre-clinical and clinical trials for further scientific validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mousikha Lala
- Department of Botany, University of North Bengal, Siliguri, India
| | - Soumita Bhattacharjee
- Department of Botany, University of North Bengal, Siliguri, India
- Department of Tea Science, University of North Bengal, Siliguri, India
| | - Chandra Ghosh
- Department of Tea Science, University of North Bengal, Siliguri, India
| | - Arnab Sen
- Department of Botany, University of North Bengal, Siliguri, India
- Biswa Bangla GenomeCentre, University of North Bengal, Siliguri, India
| | - Indrani Sarkar
- Department of Botany, University of North Bengal, Siliguri, India
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27
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Huang Y, Wu Y, Yin H, Du L, Chen C. Senkyunolide I: A Review of Its Phytochemistry, Pharmacology, Pharmacokinetics, and Drug-Likeness. Molecules 2023; 28:molecules28083636. [PMID: 37110869 PMCID: PMC10144034 DOI: 10.3390/molecules28083636] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Senkyunolide I (SI) is a natural phthalide that has drawn increasing interest for its potential as a cardio-cerebral vascular drug candidate. In this paper, the botanical sources, phytochemical characteristics, chemical and biological transformations, pharmacological and pharmacokinetic properties, and drug-likeness of SI are reviewed through a comprehensive literature survey, in order to provide support for its further research and applications. In general, SI is mainly distributed in Umbelliferae plants, and it is relatively stable to heat, acid, and oxygen, with good blood-brain barrier (BBB) permeability. Substantial studies have established reliable methods for the isolation, purification, and content determination of SI. Its pharmacological effects include analgesic, anti-inflammatory, antioxidant, anti-thrombotic, anti-tumor effects, alleviating ischemia-reperfusion injury, etc. Pharmacokinetic parameters indicate that its metabolic pathway is mainly phase Ⅱ metabolism, and it is rapidly absorbed in vivo and widely distributed in the kidneys, liver, and lungs.
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Affiliation(s)
- Yan Huang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yan Wu
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Hongxiang Yin
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Leilei Du
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Chu Chen
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
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28
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Asif M, Alvi SS, Azaz T, Khan AR, Tiwari B, Hafeez BB, Nasibullah M. Novel Functionalized Spiro [Indoline-3,5'-pyrroline]-2,2'dione Derivatives: Synthesis, Characterization, Drug-Likeness, ADME, and Anticancer Potential. Int J Mol Sci 2023; 24:ijms24087336. [PMID: 37108498 PMCID: PMC10139052 DOI: 10.3390/ijms24087336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/29/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
A highly stereo-selective, one-pot, multicomponent method was chosen to synthesize the novel functionalized 1, 3-cycloaddition spirooxindoles (SOXs) (4a-4h). Synthesized SOXs were analyzed for their drug-likeness and ADME parameters and screened for their anticancer activity. Our molecular docking analysis revealed that among all derivatives of SOXs (4a-4h), 4a has a substantial binding affinity (∆G) -6.65, -6.55, -8.73, and -7.27 Kcal/mol with CD-44, EGFR, AKR1D1, and HER-2, respectively. A functional study demonstrated that SOX 4a has a substantial impact on human cancer cell phenotypes exhibiting abnormality in cytoplasmic and nuclear architecture as well as granule formation leading to cell death. SOX 4a treatment robustly induced reactive oxygen species (ROS) generation in cancer cells as observed by enhanced DCFH-DA signals. Overall, our results suggest that SOX (4a) targets CD-44, EGFR, AKR1D1, and HER-2 and induces ROS generation in cancer cells. We conclude that SOX (4a) could be explored as a potential chemotherapeutic molecule against various cancers in appropriate pre-clinical in vitro and in vivo model systems.
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Affiliation(s)
- Mohd Asif
- Department of Chemistry, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Sahir Sultan Alvi
- Department of Immunology and Microbiology, South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Tazeen Azaz
- Department of Biological and Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS-Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Bhoopendra Tiwari
- Department of Biological and Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS-Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Bilal Bin Hafeez
- Department of Immunology and Microbiology, South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Malik Nasibullah
- Department of Chemistry, Integral University, Lucknow 226026, Uttar Pradesh, India
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Sayed Murad HA, M Rafeeq M, Alqahtani SM, S. Rajab B, Alghamdi S, J. Almehmadi S, Alam Q. Molecular docking analysis of AGTR1 antagonists. Bioinformation 2023; 19:284-289. [PMID: 37808379 PMCID: PMC10557450 DOI: 10.6026/97320630019284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 10/10/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death and morbidity globally. The renin-angiotensin system is an important regulatory system for maintaining cardiovascular and renal function. Therefore, angiotensin-converting enzyme inhibitors and angiotensin receptor blockers have emerged as first-line treatments for conditions such as hypertension and heart failure. Currently available synthetic medications used to treat various CVDs have been linked with various adverse effects. Therefore, this study focuses on targeting type-1 angiotensin II receptor (AGTR1) by natural compounds. The ZINC database natural compounds and standard AGTR1 inhibitors have been screened against the AGTR1 active site. The results showed that five compounds, namely ZINC85625504, ZINC62001623, ZINC70666587, ZINC06624086, and ZINC95486187, had similar binding energies to established AGTR1 inhibitors. These compounds were found to interact with crucial AGTR1 residues, indicating their potential as AGTR1 inhibitors. Moreover, the hit compounds demonstrated favorable drug-like characteristics and warrant further investigation for their potential use in managing CVD.
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Affiliation(s)
- Hussam Aly Sayed Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Misbahuddi M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Bodour S. Rajab
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Samah J. Almehmadi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Zinj, Bahrain
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Ilieva Y, Momekov G, Zaharieva MM, Marinov T, Kokanova-Nedialkova Z, Najdenski H, Nedialkov PT. Cytotoxic and Antibacterial Prenylated Acylphloroglucinols from Hypericum olympicum L. Plants (Basel) 2023; 12:1500. [PMID: 37050127 PMCID: PMC10097024 DOI: 10.3390/plants12071500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Two new bicyclo[3.3.1]nonane type bicyclic polyprenylated acylphloroglucinol derivatives (BPAPs), olympiforin A and B as well as three known prenylated phloroglucinols, were isolated from the aerial parts of Hypericum olympicum L. The structures of the isolated compounds were established by means of spectral techniques (HRESIMS and 1D and 2D NMR). All compounds were tested on a panel of human tumor (MDA-MB-231, EJ, K-562, HL-60 and HL-60/DOX) and non- tumorigenic (HEK-293 and EA.hy926) cell lines using the MTT assay. All tested compounds exerted significant in vitro cytotoxicity with IC50 values ranging from 1.2 to 24.9 μM and from 0.9 to 34 μM on tumor and non-cancerous cell lines, respectively. Most of the compounds had good selectivity and were more cytotoxic to the tumor cell lines than to the normal ones. A degradation of the precursor caspase 9 for some of the compounds was observed; therefore, the intrinsic pathway of apoptosis is the most likely mechanism of cytotoxic activity. The BPAPs were examined for antibacterial and antibiofilm activity through the broth microdilution method and the protocol of Stepanović. They showed a moderate effect against Enterococcus faecalis and Streptococcus pyogenes but a very profound activity against Staphylococcus aureus with minimum inhibitory concentrations (MIC) in the range of 0.78-2 mg/L. Olympiforin B also had a great effect against methicillin-resistant S. aureus (MRSA) with an MIC value of 1 mg/L and a very significant antibiofilm activity on that strain with a minimum biofilm inhibition concentration (MBIC) value of 0.5 mg/L. The structures of the isolated compounds were in silico evaluated using ADME and drug likeness tests.
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Affiliation(s)
- Yana Ilieva
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (Y.I.); (M.M.Z.)
| | - Georgi Momekov
- Department of Pharmacology, Toxicology and Pharmacotherapy, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria;
| | - Maya Margaritova Zaharieva
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (Y.I.); (M.M.Z.)
| | - Teodor Marinov
- Pharmacognosy Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | | | - Hristo Najdenski
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (Y.I.); (M.M.Z.)
| | - Paraskev T. Nedialkov
- Pharmacognosy Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
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Thapa R, Flores R, Cheng KH, Mochona B, Sikazwe D. Design and Synthesis of New Acyl Urea Analogs as Potential σ1R Ligands. Molecules 2023; 28:2319. [PMID: 36903567 PMCID: PMC10005056 DOI: 10.3390/molecules28052319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
In search of synthetically accessible open-ring analogs of PD144418 or 5-(1-propyl-1,2,5,6-tetrahydropyridin-3-yl)-3-(p-tolyl)isoxazole, a highly potent sigma-1 receptor (σ1R) ligand, we herein report the design and synthesis of sixteen arylated acyl urea derivatives. Design aspects included modeling the target compounds for drug-likeness, docking at σ1R crystal structure 5HK1, and contrasting the lower energy molecular conformers with that of the receptor-embedded PD144418-a molecule we opined that our compounds could mimic pharmacologically. Synthesis of our acyl urea target compounds was achieved in two facile steps which involved first generating the N-(phenoxycarbonyl) benzamide intermediate and then coupling it with the appropriate amines weakly to strongly nucleophilic amines. Two potential leads (compounds 10 and 12, with respective in vitro σ1R binding affinities of 2.18 and 9.54 μM) emerged from this series. These leads will undergo further structure optimization with the ultimate goal of developing novel σ1R ligands for testing in neurodegeneration models of Alzheimer's disease (AD).
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Affiliation(s)
- Rajesh Thapa
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA
| | - Rafael Flores
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA
| | - Kwan H. Cheng
- Department of Physics and Astronomy and Neuroscience Program, Trinity University, San Antonio, TX 78212, USA
| | - Bereket Mochona
- Department of Chemistry, Florida A&M University, Tallahassee, FL 32307, USA
| | - Donald Sikazwe
- Pharmaceutical Sciences Department, Feik School of Pharmacy, University of the Incarnate Word, San Antonio, TX 78209, USA
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Hussein YT, Azeez YH. DFT analysis and in silico exploration of drug-likeness, toxicity prediction, bioactivity score, and chemical reactivity properties of the urolithins. J Biomol Struct Dyn 2023; 41:1168-1177. [PMID: 34931599 DOI: 10.1080/07391102.2021.2017350] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Urolithins (Uro) are human microflora-derived metabolites of ellagic acid and ellagitannins. It has been shown to be a powerful modulator of oxidative stress, agents with potential anti-inflammatory, antiproliferative, and antiaging properties. The present study aimed to explore the drug-likeness, toxicity, and bioactivity score of urolithins that were required to be considered oral drug-active using the web-based softwares, Molinspiration, and protox_II. In addition, the chemical reactivity descriptors of the urolithins (Uro A, Uro B, Uro, C, Uro D) were also determined through density functional (DFT) calculations. Furthermore, electrostatic potential (MEP), natural bonds orbitals (NBO), HOMO-LUMO energies, chemical reactivity descriptors, dipole moment, and Fukui functions of all the urolithins were investigated by resorting the conceptual of DFT at the M06-2X/6-311++G (d, p) basis set as a tool to analyse and comprehend the molecular interaction. The results showed that all the urolithins comply with the Lipinski's rule of five and have biological activity. According to the toxicity predictions, Uro A, Uro C, and Uro D belong to class 4 while Uro B belongs to class 6. The chemical reactivity and stability features of the investigated compounds were evaluated using global chemical reactivity descriptors calculated from the Frontier Molecular Orbitals (FMOs) energies gap, which revealed that the stability order of the molecules was Uro B > Uro C > Uro D > Uro A. The present findings indicate that the urolithins could be a promising candidate for development into a therapeutic medication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yousif Taha Hussein
- Medical Laboratory Science, Technical College of Applied Sciences, Research Center, Sulaimani Polytechnic University, Sulaimani, Iraq
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Chowdhury H, Kumar Bera A, Subhasmita Raut S, Chandra Malick R, Sekhar Swain H, Saha A, Kumar Das B. In Vitro Antibacterial Efficacy of Cymbopogon flexuosus Essential Oil against Aeromonas hydrophila of Fish Origin and in Silico Molecular Docking of the Essential Oil Components against DNA Gyrase-B and Their Drug-Likeness. Chem Biodivers 2023; 20:e202200668. [PMID: 36799768 DOI: 10.1002/cbdv.202200668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
In aquaculture, diseases caused by the Aeromonads with high antibiotic resistance are among the most common and troublesome diseases. Application of herbs is emerging as a tool in controlling these diseases. Plant extracts besides disease control, favor various physiological activities in fish. In this study, essential oil of Cymbopogon flexuosus (Poaceae family) was studied in vitro for its antibacterial efficacy against two oxytetracycline (OTC) resistant and one sensitive strains of Aeromonas hydrophila. The oil was found rich (86.93 %) in oxygenated terpenoids containing 74.15 % of citral. The oil exhibited dose dependent growth inhibition of the bacteria. Mean MIC value of the oil against the sensitive strain was recorded as 2.0 mg mL-1 whereas MBC value was recorded as 4.0 mg mL-1 . The oil was found effective against the OTC resistant isolates with the MIC and MBC values ranging from 2.67-3.33 and 4.0-6.67 mg mL-1 , respectively. In silico molecular docking of the essential oil components against DNA gyrase-B, a vital macromolecule in bacterial cell, was carried out to computationally asses the efficacy of the oil against the bacteria. Some of the components of the essential oil strongly bonded with the enzyme to inhibit its efficacy. Binding energy of some components of the oil was comparable to that of the conventional antibiotic, OTC. The identified phytochemicals exhibited favorable physicochemical and pharmacokinetic properties and satisfied the rule of five (Ro5).
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Affiliation(s)
- Hemanta Chowdhury
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Asit Kumar Bera
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Subhashree Subhasmita Raut
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Ramesh Chandra Malick
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Himanshu Sekhar Swain
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Ajoy Saha
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Basanta Kumar Das
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
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Zargar S, Wani TA, Rizwan Ahamad S. An Insight into Wheat Germ Oil Nutrition, Identification of Its Bioactive Constituents and Computer-Aided Multidimensional Data Analysis of Its Potential Anti-Inflammatory Effect via Molecular Connections. Life (Basel) 2023; 13:life13020526. [PMID: 36836883 PMCID: PMC9960255 DOI: 10.3390/life13020526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Wheat germ oil (WGO) is the richest source of unexplored antioxidants and anti-inflammatory compounds. In this study, we identified the constituents of WGO by gas chromatography-mass spectrometry (GC-MS). The physicochemical and pharmacokinetic behaviors were evaluated for the top 12 constituents with the common target FABP4. Three fatty acids with significant anti-inflammatory activity were evaluated for their interaction with FABP4 by molecular docking. The molecular mechanisms involved in anti-inflammatory responses were analyzed by various in-silico analytical tools and multidimensional data analysis. WGO showed anti-inflammatory activities via FABP4 interacting physically with target genes (77.84%) and by co-expressing with 8.01% genes. Primary targets for inflammatory pathways were PPARα, PPARγ, LPL, LEP, and ADIPOQ, as depicted by gene network enrichment analysis. The key pathways implicated were the metabolism of lipids, PPAR signaling, cellular response to alcohol, oxygen and nitrogen pathway, inflammatory response pathway, and regulation of the inflammatory pathway. The common transcription factors implicated were HNF1, AP2α, CEBP, FOX, STATS, MYC, Zic, etc. In this study, we found that WGO possesses anti-inflammatory potential via FABP4 binding to PPARα, PPARγ, LPL, LEP, and ADIPOQ gene expression by regulatory transcription factors HNF, AP2α, and CEPB.
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Affiliation(s)
- Seema Zargar
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
- Correspondence:
| | - Tanveer A. Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Syed Rizwan Ahamad
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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Mangiatordi GF, Cavalluzzi MM, Delre P, Lamanna G, Lumuscio MC, Saviano M, Majoral JP, Mignani S, Duranti A, Lentini G. Endocannabinoid Degradation Enzyme Inhibitors as Potential Antipsychotics: A Medicinal Chemistry Perspective. Biomedicines 2023; 11:biomedicines11020469. [PMID: 36831006 PMCID: PMC9953700 DOI: 10.3390/biomedicines11020469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
The endocannabinoid system (ECS) plays a very important role in numerous physiological and pharmacological processes, such as those related to the central nervous system (CNS), including learning, memory, emotional processing, as well pain control, inflammatory and immune response, and as a biomarker in certain psychiatric disorders. Unfortunately, the half-life of the natural ligands responsible for these effects is very short. This perspective describes the potential role of the inhibitors of the enzymes fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MGL), which are mainly responsible for the degradation of endogenous ligands in psychic disorders and related pathologies. The examination was carried out considering both the impact that the classical exogenous ligands such as Δ9-tetrahydrocannabinol (THC) and (-)-trans-cannabidiol (CBD) have on the ECS and through an analysis focused on the possibility of predicting the potential toxicity of the inhibitors before they are subjected to clinical studies. In particular, cardiotoxicity (hERG liability), probably the worst early adverse reaction studied during clinical studies focused on acute toxicity, was predicted, and some of the most used and robust metrics available were considered to select which of the analyzed compounds could be repositioned as possible oral antipsychotics.
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Affiliation(s)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Pietro Delre
- Institute of Crystallography, National Research Council of Italy, Via G. Amendola 122/O, 70126 Bari, Italy
| | - Giuseppe Lamanna
- Institute of Crystallography, National Research Council of Italy, Via G. Amendola 122/O, 70126 Bari, Italy
- Department of Chemistry, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Maria Cristina Lumuscio
- Institute of Crystallography, National Research Council of Italy, Via G. Amendola 122/O, 70126 Bari, Italy
| | - Michele Saviano
- Institute of Crystallography, National Research Council of Italy, Via Vivaldi 43, 81100 Caserta, Italy
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 Route de Narbonne, CEDEX 4, 31077 Toulouse, France
- Université Toulouse, 118 Route de Narbonne, CEDEX 4, 31077 Toulouse, France
| | - Serge Mignani
- CERMN (Centre d’Etudes et de Recherche sur le Médicament de Normandie), Université de Caen, 14032 Caen, France
- CQM—Centro de Química da Madeira, MMRG (Molecular Materials Research Group), Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
| | - Andrea Duranti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza del Rinascimento 6, 61029 Urbino, Italy
- Correspondence: ; Tel.: +39-0722-303501
| | - Giovanni Lentini
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
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Stepanić V, Kučerová-Chlupáčová M. Review and Chemoinformatic Analysis of Ferroptosis Modulators with a Focus on Natural Plant Products. Molecules 2023; 28. [PMID: 36677534 DOI: 10.3390/molecules28020475] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 01/06/2023]
Abstract
Ferroptosis is a regular cell death pathway that has been proposed as a suitable therapeutic target in cancer and neurodegenerative diseases. Since its definition in 2012, a few hundred ferroptosis modulators have been reported. Based on a literature search, we collected a set of diverse ferroptosis modulators and analyzed them in terms of their structural features and physicochemical and drug-likeness properties. Ferroptosis modulators are mostly natural products or semisynthetic derivatives. In this review, we focused on the abundant subgroup of polyphenolic modulators, primarily phenylpropanoids. Many natural polyphenolic antioxidants have antiferroptotic activities acting through at least one of the following effects: ROS scavenging and/or iron chelation activities, increased GPX4 and NRF2 expression, and LOX inhibition. Some polyphenols are described as ferroptosis inducers acting through the generation of ROS, intracellular accumulation of iron (II), or the inhibition of GPX4. However, some molecules have a dual mode of action depending on the cell type (cancer versus neural cells) and the (micro)environment. The latter enables their successful use (e.g., apigenin, resveratrol, curcumin, and EGCG) in rationally designed, multifunctional nanoparticles that selectively target cancer cells through ferroptosis induction.
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Fan C, Wang X, Ling T, Yang Y, Zhao H. Characterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness. RNA Biol 2023; 20:431-443. [PMID: 37415294 DOI: 10.1080/15476286.2023.2231708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
Recent studies suggest RNAs act as promising drug targets. However, limited development has been achieved in detecting RNA-ligand interactions. To guide the discovery of RNA-binding ligands, it is necessary to characterize them comprehensively, especially in the binding specificity, binding affinity and drug-like properties. We established a database, RNALID (http://biomed.nscc-gz.cn/RNALID/html/index.html#/database), which collects RNA-ligand interactions validated by low-throughput experiment. RNALID contains 358 RNA-ligand interactions. Comparing to the fellow database, 94.5% of ligands in RNALID are completely or partially novel collections, and 51.78% have novel two-dimensional (2D) structures. Through the analysis of ligand structure, binding affinity and cheminformatic parameters we found that multivalent (MV) ligands mainly binding to RNA repeats are more structurally conserved in both 2D and 3D structures than other ligand types, exhibit higher binding specificity and binding affinity than ligands binding to non-repeat RNAs, but deviate far from the Lipinski's rule of five. In contrary, small molecule (SM) ligands binding to virus RNA exhibit higher affinity and more resemble protein-ligands, but potentially possess low binding specificity. Further analysis on 28 detailed drug-likeness properties indicated that RNA-ligands' development need to balance between the binding affinity and the drug-likeness because of the significant linear co-relationship between the two. Comparing RNALID ligands to FDA-approved drugs and ligands without bioactivity indicated that RNA-binding ligands are different from them in chemical properties, structural properties and drug-likeness. Thus, characterizing the RNA-ligand interactions in RNALID in multiple respects provides new insights into discovering and designing druggable ligands binding with RNA.
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Affiliation(s)
- Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, Guangdong, China
| | - Xin Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tianze Ling
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yuedong Yang
- National Computer Center in Guang Zhou, Guangzhou, Guangdong, China
- School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, Guangdong, China
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Yilmaz ZN, Dede B. Synthesis, characterization of a novel molecule containing imine group, investigation of its quantum chemical, molecular docking and ADME properties. J Biomol Struct Dyn 2022; 40:13727-13737. [PMID: 34709142 DOI: 10.1080/07391102.2021.1993339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this study, a novel Schiff base, 2-[(4-dimethylamino-benzylidene)-amino]-3-(4-hydroxy-phenyl)-propionic acid (DMAT) was synthesized as a result of the condensation reaction of N,N-dimethylamino benzaldehyde and L-tyrosine. The structure of the molecule obtained was characterized by 1H- and 13C-NMR, FTIR, UV-Vis spectroscopy and elemental analysis. Density functional theory (DFT) was used to calculate the optimized geometry, vibrational wavenumbers and electronic parameters at the B3LYP level using 6-311 G(d,p) basis set. In addition, 1H- and 13C-NMR, FTIR and UV-Vis data of the DMAT molecule were calculated with the same DFT/B3LYP/6-311G(d,p) trinity and the spectra obtained from these calculations were compared to the experimental data. The interactions of the DMAT molecule with vascular endothelial growth factor receptor-2 (VEGFR-2) and β-ketoacyl synthase (KAS III) proteins were investigated by molecular docking studies. The results obtained were then compared with the molecular docking results of the selected drug active substances Regorafenib and Isoniazid molecules. The best interaction was between DMAT-VEGFR-2 with -8.30 and -1586.97 kcal/mol binding energy and full fitness score, respectively. In addition, ADME properties of the DMAT molecule were examined and some drug-likeness, physicochemical, lipophilicity and pharmacokinetic properties of this molecule were determined. The ADME and Lipinski parameters of the DMAT molecule exhibited good drug-likeness properties.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zeliha Nur Yilmaz
- Faculty of Science & Art, Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
| | - Bülent Dede
- Faculty of Science & Art, Department of Chemistry, Süleyman Demirel University, Isparta, Turkey
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Argirova M, Guncheva M, Momekov G, Cherneva E, Mihaylova R, Rangelov M, Todorova N, Denev P, Anichina K, Mavrova A, Yancheva D. Modulation Effect on Tubulin Polymerization, Cytotoxicity and Antioxidant Activity of 1H-Benzimidazole-2-Yl Hydrazones. Molecules 2022; 28:molecules28010291. [PMID: 36615483 PMCID: PMC9822270 DOI: 10.3390/molecules28010291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022]
Abstract
1H-benzimidazol-2-yl hydrazones with varying hydroxy and methoxy phenyl moieties were designed. Their effect on tubulin polymerization was evaluated in vitro on porcine tubulin. The compounds elongated the nucleation phase and slowed down the tubulin polymerization comparably to nocodazole. The possible binding modes of the hydrazones with tubulin were explored by molecular docking at the colchicine binding site. The anticancer activity was evaluated against human malignant cell lines MCF-7 and AR-230, as well as against normal fibroblast cells 3T3 and CCL-1. The compounds demonstrated a marked antineoplastic activity in low micromolar concentrations in both screened in vitro tumor models. The most active were the trimethoxy substituted derivative 1i and the positional isomers 1j and 1k, containing hydroxy and methoxy substituents: they showed IC50 similar to the reference podophyllotoxin in both tumor cell lines, accompanied with high selectivity towards the malignantly transformed cells. The compounds exerted moderate to high ability to scavenge peroxyl radicals and certain derivatives-1l containing metha-hydroxy and para-methoxy group, and 1b-e with di/trihydroxy phenyl moiety, revealed HORAC values high or comparable to those of well-known phenolic antioxidants. Thus the 1H-benisimidazol-2-yl hydrazones with hydroxy/methoxy phenyl fragments were recognized as new agents exhibiting promising combined antioxidant and antineoplastic action.
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Affiliation(s)
- Maria Argirova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Maya Guncheva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Georgi Momekov
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Emiliya Cherneva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Rositsa Mihaylova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Miroslav Rangelov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Nadezhda Todorova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Petko Denev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Kameliya Anichina
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria
| | - Anelia Mavrova
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 1756 Sofia, Bulgaria
| | - Denitsa Yancheva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence:
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Shree P, Mishra P, Kumar P, Pandey H, Giri R, Chaube R, Garg N, Tripathi YB. In silico screening of Pueraria tuberosa (PTY-2) for targeting COVID-19 by countering dual targets M pro and TMPRSS2. J Biomol Struct Dyn 2022; 40:11611-11624. [PMID: 34424815 DOI: 10.1080/07391102.2021.1965029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
COVID-19 pandemic was started in Wuhan city of China in December 2019; immensely affected global population. Herein, an effort was made to identify potential inhibitors from active phytochemicals of Pueraria tuberosa (PTY-2) via molecular docking study. Our study showed five potential inhibitors (Robinin, Genistin, Daidzin, Hydroxytuberosone, Tuberostan) against Mpro and five inhibitors (Robinin, Anhydrotuberosin, Daidzin, Hydroxytuberosone, Stigmasterol) against TMPRSS2. Out of these, Robinin, Daidzin and Hydroxytuberosone were common inhibitors for Mpro and TMPRSS2. Among these, Robinin showed the highest binding affinity, therefore, tested for MD simulation runs and found stable. ADMET analysis revealed the best-docked compounds are safe and follow the Lipinski Rule of Five. Thus, it could be suggested that phytochemicals of PTY-2 could serve as potential inhibitors for COVID-19 targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priya Shree
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priyanka Mishra
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, India
| | - Harsh Pandey
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, India
| | - Radha Chaube
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Neha Garg
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Yamini Bhusan Tripathi
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Choudhir G, Sharma S, Hariprasad P. A combinatorial approach to screen structurally diverse acetylcholinesterase inhibitory plant secondary metabolites targeting Alzheimer's disease. J Biomol Struct Dyn 2022; 40:11705-11718. [PMID: 34351840 DOI: 10.1080/07391102.2021.1962408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD) is a form of Dementia known to diminish the brain's function by perturbating its structural and functional components. Though cholinesterase inhibitors are widely used to treat AD, they are limited by numbers and side effects. Hence, present study aims to identify structurally diverse Acetylcholinesterase (AChE) inhibitory plant secondary metabolites (PSM) by employing high throughput screening and computational studies. AChE inhibitory activity was performed using 390 crude extracts from 63 plant parts belongs to 58 plants. The lowest IC50 value was recorded by acetone extract of Cyperus rotundus rhizome at 0.5 mg/ml, followed by methanol extract of Terminalia arjuna bark (0.95 mg/ml) and water extract Acacia catechu stem (0.95 mg/ml). A virtual library containing 487 PSM belongs to 18 plants found positive for AChE inhibition (IC50≤5 mg/ml) was prepared. Through ADMET analysis, 78 PSM fulfilling selected drug-likeness parameters were selected for further analysis. Molecular docking studies of selected PSM against AChE recorded a wide range of binding energy from -3.40 to -10.90 Kcal/mol. Further molecular dynamics simulation studies also recorded stabilized interactions of AChE-ligand complexes in the term of RMSD, RMSF, Rg, SASA, and hydrogen bond interaction. MMPBSA analysis revealed the binding energy of selected PSM ranging from -123.757 to -261.697 kJ/mol. Our study demonstrated the potential of 12 PSM (Sugiol, Margolone, 7-Hydroxy-3',4'-(Methylenedioxy) flavan, Beta-cyprone, Ethenone, Isomargolonone, Serpentine, Cryptolepine, Rotundone, Strictamin, Rotundenol and Nootkatone) as AChE inhibitors. Further in vitro and in vivo experimental evaluations with pure PSM could be beneficial for therapeutic uses.
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Affiliation(s)
- Gourav Choudhir
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Satyawati Sharma
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - P Hariprasad
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
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Ciftci H, Sever B, Kaya N, Bayrak N, Yıldız M, Yıldırım H, Tateishi H, Otsuka M, Fujita M, TuYuN AF. Studies on 1,4-Quinone Derivatives Exhibiting Anti-Leukemic Activity along with Anti-Colorectal and Anti-Breast Cancer Effects. Molecules 2022; 28. [PMID: 36615273 DOI: 10.3390/molecules28010077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC), breast cancer, and chronic myeloid leukemia (CML) are life-threatening malignancies worldwide. Although potent therapeutic and screening strategies have been developed so far, these cancer types are still major public health problems. Therefore, the exploration of more potent and selective new agents is urgently required for the treatment of these cancers. Quinones represent one of the most important structures in anticancer drug discovery. We have previously identified a series of quinone-based compounds (ABQ-1-17) as anti-CML agents. In the current work, ABQ-3 was taken to the National Cancer Institute (NCI) for screening to determine its in vitro antiproliferative effects against a large panel of human tumor cell lines at five doses. ABQ-3 revealed significant growth inhibition against HCT-116 CRC and MCF-7 breast cancer cells with 2.00 µM and 2.35 µM GI50 values, respectively. The MTT test also showed that ABQ-3 possessed anticancer effects towards HCT-116 and MCF-7 cells with IC50 values of 5.22 ± 2.41 μM and 7.46 ± 2.76 μM, respectively. Further experiments indicated that ABQ-3 induced apoptosis in both cell lines, and molecular docking studies explicitly suggested that ABQ-3 exhibited DNA binding in a similar fashion to previously reported compounds. Based on in silico pharmacokinetic prediction, ABQ-3 might display drug-like features enabling this compound to become a lead molecule for future studies.
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Akdağ K, Tok F, Karakuş S, Erdoğan Ö, Çevik Ö, Koçyiğit-Kaymakçıoğlu B. Synthesis and Biological Evaluation of Some Hydrazide-Hydrazone Derivatives as Anticancer Agents. Acta Chim Slov 2022; 69:863-875. [PMID: 36562164 DOI: 10.17344/acsi.2022.7614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/04/2022] [Accepted: 10/30/2022] [Indexed: 12/14/2022] Open
Abstract
In this study, a series of hydrazide-hydrazone derivatives (3a-3u) were synthesized and evaluated for their anticancer activities against prostate cancer cell line (PC-3), breast cancer cell line (MCF-7), colon cancer cell line (HT-29) and human umbilical vein endothelial cells (HUVEC) using MTT assay. In particular, compound 3h having a pyrrole ring was found to be the most potent derivative with IC50 = 1.32, 2.99, 1.71 µM against PC-3, MCF-7, HT-29 cancer cell lines respectively using paclitaxel as a standard compound. Furthermore, compound 3h was subjected to further biological studies such as caspase-3 activity and Annexin-V assay to evaluate their inhibitory potentials. The activity results displayed that compound 3h increased caspase-3 activation and the number of cells to early apoptosis. The additional studies like pharmacokinetics, bioavailability scores and drug-likeness properties were also evaluated. The in silico pharmacokinetics predictions displayed that the bioavailability of these compounds may be high.
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Affiliation(s)
- Kadriye Akdağ
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, 34854, Istanbul, Turkey.
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Vila N, Besada P, Brea J, Loza MI, Terán C. Novel Phthalazin-1(2H)-One Derivatives Displaying a Dithiocarbamate Moiety as Potential Anticancer Agents. Molecules 2022; 27. [PMID: 36500208 DOI: 10.3390/molecules27238115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
Nowadays, cancer disease seems to be the second most common cause of death worldwide. Molecular hybridization is a drug design strategy that has provided promising results against multifactorial diseases, including cancer. In this work, two series of phthalazinone-dithiocarbamate hybrids were described, compounds 6-8, which display the dithiocarbamate scaffold at N2, and compounds 9, in which this moiety was placed at C4. The proposed compounds were successfully synthesized via the corresponding aminoalkyl phthalazinone derivatives and using a one-pot reaction with carbon disulfide, anhydrous H3PO4, and different benzyl or propargyl bromides. The antiproliferative effects of the titled compounds were explored against three human cancer cell lines (A2780, NCI-H460, and MCF-7). The preliminary results revealed significant differences in activity and selectivity depending on the dithiocarbamate moiety location. Thus, in general terms, compounds 6-8 displayed better activity against the A-2780 and MCF-7 cell lines, while most of the analogues of the 9 group were selective toward the NCI-H460 cell line. Compounds 6e, 8e, 6g, 9a-b, 9d, and 9g with IC50 values less than 10 µM were the most promising. The drug-likeness and toxicity properties of the novel phthalazinone-dithiocarbamate hybrids were predicted using Swiss-ADME and ProTox web servers, respectively.
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Ticona JC, Bilbao-Ramos P, Amesty Á, Flores N, Dea-Ayuela MA, Bazzocchi IL, Jiménez IA. Flavonoids from Piper Species as Promising Antiprotozoal Agents against Giardia intestinalis. Structure-Activity Relationship and Drug-Likeness Studies. Pharmaceuticals (Basel) 2022; 15:1386. [PMID: 36355559 PMCID: PMC9695682 DOI: 10.3390/ph15111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2023] Open
Abstract
Diarrhea diseases caused by the intestinal protozoan parasite Giardia intestinalis are a major global health burden. Moreover, there is an ongoing need for novel anti-Giardia drugs due to drawbacks with currently available treatments. This paper reports on the isolation and structural elucidation of six new flavonoids (1-6), along with twenty-three known ones (7-29) from the Piper species. Their structures were established by spectroscopic and spectrometric techniques. Flavonoids were tested for in vitro antiprotozoal activity against Giardia intestinalis trophozoites. In addition, structure-activity relationship (SAR) and in silico ADME studies were performed to understand the pharmacophore and pharmacokinetic properties of these natural compounds. Eight flavonoids from this series exhibited remarkable activity in the micromolar range. Moreover, compound 4 was identified as having a 40-fold greater antiparasitic effect (IC50 61.0 nM) than the clinical reference drug, metronidazole (IC50 2.5 µM). This antiprotozoal potency was coupled with an excellent selectivity index (SI 233) on murine macrophages and in silico drug-likeness. SAR studies revealed that the substitution patterns, type of functional group, and flavonoid skeleton played an essential role in the activity. These findings highlight flavonoid 4 as a promising candidate to develop new drugs for the treatment of Giardia infections.
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Affiliation(s)
- Juan C. Ticona
- Instituto Universitario de Bio-Orgánica Antonio González, Departamento de Química Orgánica, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain
- Instituto de Investigaciones Fármaco Bioquímicas, Facultad de Ciencias Farmacéuticas y Bioquímicas, Universidad Mayor de San Andrés, Avenida Saavedra 2224, Miraflores, La Paz, Bolivia
| | - Pablo Bilbao-Ramos
- Departamento de Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Ángel Amesty
- Instituto Universitario de Bio-Orgánica Antonio González, Departamento de Química Orgánica, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain
| | - Ninoska Flores
- Instituto de Investigaciones Fármaco Bioquímicas, Facultad de Ciencias Farmacéuticas y Bioquímicas, Universidad Mayor de San Andrés, Avenida Saavedra 2224, Miraflores, La Paz, Bolivia
| | - M. Auxiliadora Dea-Ayuela
- Departamento de Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
- Departamento de Farmacia, Bioquímica y Biología Molecular, Universidad CEU-Cardenal Herrera, Avda. Seminario s/n, 46113 Moncada, Valencia, Spain
| | - Isabel L. Bazzocchi
- Instituto Universitario de Bio-Orgánica Antonio González, Departamento de Química Orgánica, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain
| | - Ignacio A. Jiménez
- Instituto Universitario de Bio-Orgánica Antonio González, Departamento de Química Orgánica, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez 2, 38206 La Laguna, Tenerife, Spain
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Degfie T, Ombito JO, Demissie TB, Eswaramoorthy R, Dekebo A, Endale M. Antibacterial and Antioxidant Activities, in silico Molecular Docking, ADMET and DFT Analysis of Compounds from Roots of Cyphostemma cyphopetalum. Adv Appl Bioinform Chem 2022; 15:79-97. [PMID: 36330228 PMCID: PMC9624657 DOI: 10.2147/aabc.s377336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Background Cyphostemma cyphopetalum is a medicinal plant traditionally used to treat various ailments. Limited studies on C. cyphopetalum inspired us to investigate the chemical nature and therapeutic potential of the plant. Methods Silica gel column chromatographic separation was used for isolation. 1D and 2D NMR spectroscopic analysis and literature data were used for structural elucidation. Agar well diffusion assay was used for evaluation of antibacterial activity against E. coli, P. aeruginosa, and S. aureus. DPPH assay was used to evaluate radical scavenging activities. Molecular docking was done by AutoDock Vina 4.2 open-source program. DFT calculations were performed using the Gaussian 16 program package. Results Dichloromethane/methanol (1:1) roots extract afforded a new hydroxyl-spongiane diterpenoid lactone derivative, 3-hydroxyisoagatholactone (1), along with β-sitosterol (2) and ε-viniferin (3) whereas methanol extract afforded trans-resveratrol (4), gnetin H (5), tricuspidatol A (6), ε-viniferin-diol (7) and parthenostilbenin B (8). At 50 μg/mL, compound 3 recorded the highest inhibition against E. coli (8.55 ± 0.45 mm) and S. aureus (9.30 ±1.39 mm). Against P. aeruginosa, compound 5 consistently outperformed chloramphenicol (11.76 ± 0.77 mm, at 30 g/mL). Maximum binding affinity were observed by compound 3 against DNA gyrase B (-7.6 kcal/mol) where as compound 5 displayed maximum binding against PqsA (-8.8 kcal/mol) and S. aureus PK (-5.8 kcal/mol). Compounds 1, 3 and 4 satisfy Lipinski’s rule of five. Trans-resveratrol (4) demonstrated strong DPPH scavenging activity at 12.5 g/mL, with IC50 values of 0.052 µg/mL, compared to ascorbic acid (IC50 value of 0.0012 µg/mL). Conclusion In this work, eight compounds were identified from the roots extracts of C. cyphopetalum including a new hydroxyl-spongiane diterpenoid lactone, 3-hydroxyisoagatholactone (1). Compounds 3 and 5 exhibited good antibacterial activity and binding affinities. The docking result is in agreement with the invitro antibacterial study. Overall, the study result suggests that the isolated compounds have the potential to be used as therapeutic agents, which supports the traditional uses of C. cyphpetalum roots.
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Affiliation(s)
- Teshome Degfie
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Japheth O Ombito
- Department of Chemistry, University of Botswana, Gaborone, Botswana
| | - Taye B Demissie
- Department of Chemistry, University of Botswana, Gaborone, Botswana
| | - Rajalakshmanan Eswaramoorthy
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Aman Dekebo
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia,Institute of Pharmaceutical Sciences, Adama Science and Technology University, Adama, Ethiopia
| | - Milkyas Endale
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia,Correspondence: Milkyas Endale; Teshome Degfie, Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia, Email ;
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Pangal A, Ahmed K. Synthesis and biological evaluation of coumarin-quinone hybrids as multifunctional bioactive agents. ADMET DMPK 2022; 11:81-96. [PMID: 36778907 PMCID: PMC9909729 DOI: 10.5599/admet.1468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/29/2022] [Indexed: 11/18/2022]
Abstract
We report the synthesis, structural characterization and pharmaceutical activity of four coumarin-quinone hybrids. The compounds were significantly active against Staphylococcus aureus, Pseudomonas aeoginosa and Candida albicans. Promising antioxidant activity was observed when compared to ascorbic acid. Two compounds, DTBSB and DTBSN, also showed commendable in vitro antiproliferative activities against the cells of human cancer cell lines MCF-7, MDA-MB-231, COLO-205, HT-29 and A549 along with appreciable tumor selectivity with distinct selectivity index. Molecular docking studies using cyclooxygenase-2 (PDB ID: 6COX) revealed strong binding affinities for the COX-2 active site. Moreover, ADMET properties of the synthesized compounds were determined using the pKCSM and SwissADME online tools and all the compounds had accurate pharmacokinetic profiles. Hence, the new coumarin-quinone hybrids DTBSB and DTBSN can be considered for optimization and lead development.
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Affiliation(s)
- Anees Pangal
- Department of Chemistry & Post Graduate Centre, Abeda Inamdar Sr. College of Arts, Science & Commerce (Autonomous), Camp, Pune – 411001, India,Advanced Scientific Research Laboratory, Azam Campus, Pune – 411001, India
| | - Khursheed Ahmed
- Department of Chemistry & Post Graduate Centre, Abeda Inamdar Sr. College of Arts, Science & Commerce (Autonomous), Camp, Pune – 411001, India,Advanced Scientific Research Laboratory, Azam Campus, Pune – 411001, India,*Corresponding Author: E-mail:
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Pradhan S, Prasad R, Sinha C, Sen P. Molecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents. J Biomol Struct Dyn 2022; 40:7129-7142. [PMID: 34060418 PMCID: PMC8171005 DOI: 10.1080/07391102.2021.1897043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/19/2021] [Indexed: 11/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19. The Sulfonamides groups have been widely introduced in several drugs, especially for their antibacterial activities and generally prescribed for respiratory infections. On the other hand, imidazole groups have the multipotency to act as drugs, including antiviral activity. We have used a structure-based drug design approach to design some imidazole derivatives of sulfonamide, which can efficiently bind to the active site of SARS-CoV-2 main protease and thus may have the potential to inhibit its proteases activity. We conducted molecular docking and molecular dynamics simulation to observe the stability and flexibility of inhibitor complexes. We have checked ADMET (absorption, distribution, metabolism, excretion and toxicity) and drug-likeness rules to scrutinize toxicity and then designed the most potent compound based on computational chemistry. Our small predicted molecule non-peptide protease inhibitors could provide a useful model in the further search for novel compounds since it has many advantages over peptidic drugs, like lower side effects, toxicity and less chance of drug resistance. Further, we confirmed the stability of our inhibitor-complex and interaction profile through the Molecular dynamics simulation study. Our small predicted moleculeCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayantan Pradhan
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Prosenjit Sen
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
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Wang J, Chu Y, Mao J, Jeon HN, Jin H, Zeb A, Jang Y, Cho KH, Song T, No KT. De novo molecular design with deep molecular generative models for PPI inhibitors. Brief Bioinform 2022; 23:6643455. [PMID: 35830870 DOI: 10.1093/bib/bbac285] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 12/27/2022] Open
Abstract
We construct a protein-protein interaction (PPI) targeted drug-likeness dataset and propose a deep molecular generative framework to generate novel drug-likeness molecules from the features of the seed compounds. This framework gains inspiration from published molecular generative models, uses the key features associated with PPI inhibitors as input and develops deep molecular generative models for de novo molecular design of PPI inhibitors. For the first time, quantitative estimation index for compounds targeting PPI was applied to the evaluation of the molecular generation model for de novo design of PPI-targeted compounds. Our results estimated that the generated molecules had better PPI-targeted drug-likeness and drug-likeness. Additionally, our model also exhibits comparable performance to other several state-of-the-art molecule generation models. The generated molecules share chemical space with iPPI-DB inhibitors as demonstrated by chemical space analysis. The peptide characterization-oriented design of PPI inhibitors and the ligand-based design of PPI inhibitors are explored. Finally, we recommend that this framework will be an important step forward for the de novo design of PPI-targeted therapeutics.
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Affiliation(s)
- Jianmin Wang
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea.,Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea
| | - Yanyi Chu
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Jiashun Mao
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea.,Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea
| | - Hyeon-Nae Jeon
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea.,Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Haiyan Jin
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea.,Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea
| | - Amir Zeb
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea.,Department of Natural and Basic Sciences, University of Turbat, 92600, Pakistan
| | - Yuil Jang
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea.,Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea
| | - Kwang-Hwi Cho
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Tao Song
- School of Computer Science and Technology, China University of Petroleum, Qingdao, 266580, Shandong, China
| | - Kyoung Tai No
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Republic of Korea.,Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Republic of Korea
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Ahangarzadeh N, Shakour N, Rezvanpoor S, Bakherad H, Pakdel MH, Farhadi G, Sepehri S. Design, synthesis, and in silico studies of tetrahydropyrimidine analogs as urease enzyme inhibitors. Arch Pharm (Weinheim) 2022; 355:e2200158. [PMID: 35833485 DOI: 10.1002/ardp.202200158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/07/2022]
Abstract
The urease enzyme, a metalloenzyme having Ni2+ ions, is recognized in some bacteria, fungi, and plants. Particularly, it is vital to the progress of infections induced by pathogenic microbes, such as Proteus mirabilis and Helicobacter pylori. Herein, we reported the synthesis of a series of tetrahydropyrimidine derivatives and evaluated their antiurease activity. Finally, quantitative and qualitative analyses of the derivatives were performed via in silico studies. Urease inhibitory activity was determined as the reaction of H. pylori urease with different concentrations of compounds, and thiourea was used as a standard compound. Docking and dynamics methodologies were applied to study the interactions of the best compounds with the amino acids in the active site. All compounds showed good to excellent antiurease activity. The potent compounds were not cytotoxic against the HUVEC normal cell line. Based on the docking study, compound 4e with the highest urease inhibitory activity (IC50 = 6.81 ± 1.42 µM) showed chelates with both Ni2+ ions of the urease active site. Further, compound 4f displayed a very good inhibitory activity (IC50 = 8.45 ± 1.64 μM) in comparison to thiourea (IC50 = 22.03 ± 1.24 μM). The molecular docking and dynamics simulation results were correlated with the in vitro assay results. Moreover, the derivatives 4a-n followed Lipinski's rule-of-five and had drug-likeness properties.
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Affiliation(s)
- Nazli Ahangarzadeh
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Neda Shakour
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadaf Rezvanpoor
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hamid Bakherad
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad H Pakdel
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ghazaleh Farhadi
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Saghi Sepehri
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran.,Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
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