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Siddique F, Anwaar A, Bashir M, Nadeem S, Rawat R, Eyupoglu V, Afzal S, Bibi M, Bin Jardan YA, Bourhia M. Revisiting methotrexate and phototrexate Zinc15 library-based derivatives using deep learning in-silico drug design approach. Front Chem 2024; 12:1380266. [PMID: 38576849 PMCID: PMC10991842 DOI: 10.3389/fchem.2024.1380266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
Introduction: Cancer is the second most prevalent cause of mortality in the world, despite the availability of several medications for cancer treatment. Therefore, the cancer research community emphasized on computational techniques to speed up the discovery of novel anticancer drugs. Methods: In the current study, QSAR-based virtual screening was performed on the Zinc15 compound library (271 derivatives of methotrexate (MTX) and phototrexate (PTX)) to predict their inhibitory activity against dihydrofolate reductase (DHFR), a potential anticancer drug target. The deep learning-based ADMET parameters were employed to generate a 2D QSAR model using the multiple linear regression (MPL) methods with Leave-one-out cross-validated (LOO-CV) Q2 and correlation coefficient R2 values as high as 0.77 and 0.81, respectively. Results: From the QSAR model and virtual screening analysis, the top hits (09, 27, 41, 68, 74, 85, 99, 180) exhibited pIC50 ranging from 5.85 to 7.20 with a minimum binding score of -11.6 to -11.0 kcal/mol and were subjected to further investigation. The ADMET attributes using the message-passing neural network (MPNN) model demonstrated the potential of selected hits as an oral medication based on lipophilic profile Log P (0.19-2.69) and bioavailability (76.30% to 78.46%). The clinical toxicity score was 31.24% to 35.30%, with the least toxicity score (8.30%) observed with compound 180. The DFT calculations were carried out to determine the stability, physicochemical parameters and chemical reactivity of selected compounds. The docking results were further validated by 100 ns molecular dynamic simulation analysis. Conclusion: The promising lead compounds found endorsed compared to standard reference drugs MTX and PTX that are best for anticancer activity and can lead to novel therapies after experimental validations. Furthermore, it is suggested to unveil the inhibitory potential of identified hits via in-vitro and in-vivo approaches.
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Affiliation(s)
- Farhan Siddique
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Ahmar Anwaar
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Maryam Bashir
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
- Southern Punjab Institute of Health Sciences, Multan, Pakistan
| | - Sumaira Nadeem
- Department of Pharmacy, The Women University, Multan, Pakistan
| | - Ravi Rawat
- School of Health Sciences & Technology, UPES University, Dehradun, India
| | - Volkan Eyupoglu
- Department of Chemistry, Cankırı Karatekin University, Cankırı, Türkiye
| | - Samina Afzal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Mehvish Bibi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
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Sayed EM, Bakhite EA, Hassanien R, Farhan N, Aly HF, Morsy SG, Hassan NA. Novel tetrahydroisoquinolines as DHFR and CDK2 inhibitors: synthesis, characterization, anticancer activity and antioxidant properties. BMC Chem 2024; 18:34. [PMID: 38365746 PMCID: PMC10873978 DOI: 10.1186/s13065-024-01139-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
In this study, we synthesized new 5,6,7,8-tetrahydroisoquinolines and 6,7,8,9-tetrahydrothieno[2,3-c]isoquinolines based on 4-(N,N-dimethylamino)phenyl moiety as expected anticancer and/or antioxidant agents. The structure of all synthesized compounds were confirmed by spectral date (FT-IR, 1H NMR, 13C NMR) and elemental analysis. We evaluated the anticancer activity of these compounds toward two cell lines: A459 cell line (lung cancer cells) and MCF7 cell line (breast cancer cells). All tested compounds showed moderate to strong anti-cancer activity towards the two cell lines. Compound 7e exhibited the most potent cytotoxic activity against A549 cell line (IC50: 0.155 µM) while compound 8d showed the most potent one against MCF7 cell line (IC50: 0.170 µM) in comparison with doxorubicin. In addition, we examined the effect of compounds 7e and 8d regarding the growth of A549 and MCF7 cell lines, employing flow cytometry and Annexin V-FITC apoptotic assay. Our results showed that compound 7e caused cell cycle arrest at the G2/M phase with a 79-fold increase in apoptosis of A459 cell line. Moreover, compound 8d caused cell cycle arrest at the S phase with a 69-fold increase in apoptosis of MCF7 cell line. Furthermore, we studied the activity of these compounds as enzyme inhibitors against several enzymes. Our findings by docking and experimental studies that compound 7e is a potent CDK2 inhibitor with IC50 of 0.149 µM, compared to the Roscovitine control drug with IC50 of 0.380 µM. We also found that compound 8d is a significant DHFR inhibitor with an IC50 of 0.199 µM, compared to Methotrexate control drug with IC50 of 0.131 µM. Evaluation of the antioxidant properties of ten compounds was also studied in comparison with Vitamin C. Compounds 1, 3, 6, 7c and 8e have higher antioxidant activity than Vitamin C which mean that these compounds can used as potent antioxidant drugs.
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Affiliation(s)
- Eman M Sayed
- Department of Chemistry, Faculty of Science, New Valley University, El-Kharja, 72511, Egypt.
| | - Etify A Bakhite
- Department of Chemistry, Faculty of Science, Assiut University, Assiut, 71516, Egypt.
| | - Reda Hassanien
- Department of Chemistry, Faculty of Science, New Valley University, El-Kharja, 72511, Egypt
| | - Nasser Farhan
- Department of Chemistry, Faculty of Science, New Valley University, El-Kharja, 72511, Egypt
| | - Hanan F Aly
- Department of Therapeutic Chemistry, National Research Centre, El-Behooth St., Dokki, Cairo, 12622, Egypt
| | - Salma G Morsy
- Department of Cancer Biology, Cancer Immunology and Virology Unit, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Nivin A Hassan
- Department Cancer Biology, Pharmacology and Experimental Oncology Unit, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
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Abdalhameid E, Abd El-Haleim EA, Abdelsalam RM, Georgy GS, Fawzy HM, Kenawy SA. Cinnamic acid mitigates methotrexate-induced lung fibrosis in rats: comparative study with pirfenidone. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:1071-1079. [PMID: 37581637 PMCID: PMC10791841 DOI: 10.1007/s00210-023-02652-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/28/2023] [Indexed: 08/16/2023]
Abstract
PURPOSE Lung fibrosis is a heterogeneous lung condition characterized by excessive accumulation of scarred tissue, leading to lung architecture destruction and restricted ventilation. The current work was conducted to examine the probable shielding influence of cinnamic acid against lung fibrosis induced by methotrexate. METHODS Rats were pre-treated with oral administration of cinnamic acid (50 mg/kg/day) for 14 days, whereas methotrexate (14 mg/kg) was orally given on the 5th and 12th days of the experiment. Pirfenidone (50 mg/kg/day) was used as a standard drug. At the end of the experiment, oxidative parameters (malondialdehyde, myeloperoxidase, nitric oxide, and total glutathione) and inflammatory mediators (tumor necrosis factor-α and interleukin-8), as well as transforming growth factor-β and collagen content, as fibrosis indicators, were measured in lung tissue. RESULTS Our results revealed that cinnamic acid, as pirfenidone, effectively prevented the methotrexate-induced overt histopathological damage. This was associated with parallel improvements in oxidative, inflammatory, and fibrotic parameters measured. The outcomes of cinnamic acid administration were more or less the same as those of pirfenidone. In conclusion, pre-treatment with cinnamic acid protects against methotrexate-induced fibrosis, making it a promising prophylactic adjuvant therapy to methotrexate and protecting against its possible induction of lung fibrosis.
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Affiliation(s)
- Eman Abdalhameid
- Department of Pharmacology and Toxicology, Egyptian Drug Authority (EDA), Giza, Egypt.
| | - Enas A Abd El-Haleim
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Rania M Abdelsalam
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Department of Biology, School of Pharmacy, Newgiza University, Giza, Egypt
| | - Gehan S Georgy
- Department of Pharmacology and Toxicology, Egyptian Drug Authority (EDA), Giza, Egypt
| | - Hala M Fawzy
- Department of Pharmacology and Toxicology, Egyptian Drug Authority (EDA), Giza, Egypt
| | - Sanaa A Kenawy
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Wu X, Ma Y, Wang L, Qin X. A Route for Investigating Psoriasis: From the Perspective of the Pathological Mechanisms and Therapeutic Strategies of Cancer. Int J Mol Sci 2023; 24:14390. [PMID: 37762693 PMCID: PMC10532365 DOI: 10.3390/ijms241814390] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Psoriasis is an incurable skin disease that develops in about two-thirds of patients before the age of 40 and requires lifelong treatment; its pathological mechanisms have not been fully elucidated. The core pathological process of psoriasis is epidermal thickening caused by the excessive proliferation of epidermal keratinocytes, which is similar to the key feature of cancer; the malignant proliferation of cancer cells causes tumor enlargement, suggesting that there is a certain degree of commonality between psoriasis and cancer. This article reviews the pathological mechanisms that are common to psoriasis and cancer, including the interaction between cell proliferation and an abnormal immune microenvironment, metabolic reprogramming, and epigenetic reprogramming. In addition, there are common therapeutic agents and drug targets between psoriasis and cancer. Thus, psoriasis and cancer share a common pathological mechanisms-drug targets-therapeutic agents framework. On this basis, it is proposed that investigating psoriasis from a cancer perspective is beneficial to enriching the research strategies related to psoriasis.
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Affiliation(s)
- Xingkang Wu
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan 030006, China; (Y.M.); (L.W.)
| | | | | | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan 030006, China; (Y.M.); (L.W.)
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Suri GS, Kaur G, Carbone GM, Shinde D. Metabolomics in oncology. Cancer Rep (Hoboken) 2023; 6:e1795. [PMID: 36811317 PMCID: PMC10026298 DOI: 10.1002/cnr2.1795] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/15/2023] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Oncogenic transformation alters intracellular metabolism and contributes to the growth of malignant cells. Metabolomics, or the study of small molecules, can reveal insight about cancer progression that other biomarker studies cannot. Number of metabolites involved in this process have been in spotlight for cancer detection, monitoring, and therapy. RECENT FINDINGS In this review, the "Metabolomics" is defined in terms of current technology having both clinical and translational applications. Researchers have shown metabolomics can be used to discern metabolic indicators non-invasively using different analytical methods like positron emission tomography, magnetic resonance spectroscopic imaging etc. Metabolomic profiling is a powerful and technically feasible way to track changes in tumor metabolism and gauge treatment response across time. Recent studies have shown metabolomics can also predict individual metabolic changes in response to cancer treatment, measure medication efficacy, and monitor drug resistance. Its significance in cancer development and treatment is summarized in this review. CONCLUSION Although in infancy, metabolomics can be used to identify treatment options and/or predict responsiveness to cancer treatments. Technical challenges like database management, cost and methodical knowhow still persist. Overcoming these challenges in near further can help in designing new treatment régimes with increased sensitivity and specificity.
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Affiliation(s)
- Gurparsad Singh Suri
- Department of Biological Sciences, California Baptist University, Riverside, California, USA
| | - Gurleen Kaur
- Department of Biological Sciences, California Baptist University, Riverside, California, USA
| | - Giuseppina M Carbone
- Institute of Oncology Research (IOR), Universita' della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Dheeraj Shinde
- Institute of Oncology Research (IOR), Universita' della Svizzera Italiana (USI), Bellinzona, Switzerland
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Seetin S, Saparpakorn P, Vanichtanankul J, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S, Hannongbua S. Key interactions of pyrimethamine derivatives specific to wild-type and mutant P. falciparum dihydrofolate reductase based on 3D-QSAR, MD simulations and quantum chemical calculations. J Biomol Struct Dyn 2022:1-16. [DOI: 10.1080/07391102.2022.2096114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Sasipha Seetin
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Patchreenart Saparpakorn
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
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Tutone M, Almerico AM. Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics. Molecules 2021; 26:molecules26247500. [PMID: 34946582 PMCID: PMC8707150 DOI: 10.3390/molecules26247500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
To date, computational approaches have been recognized as a key component in drug design and discovery workflows [...].
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Alam MS, Saleh MA, Mozibullah M, Riham AT, Solayman M, Gan SH. Computational algorithmic and molecular dynamics study of functional and structural impacts of non-synonymous single nucleotide polymorphisms in human DHFR gene. Comput Biol Chem 2021; 95:107587. [PMID: 34710812 DOI: 10.1016/j.compbiolchem.2021.107587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/21/2021] [Accepted: 10/01/2021] [Indexed: 11/26/2022]
Abstract
Human dihydrofolate reductase (DHFR) is a conserved enzyme that is central to folate metabolism and is widely targeted in pathogenic diseases as well as cancers. Although studies have reported the fact that genetic mutations in DHFR leads to a rare autosomal recessive inborn error of folate metabolism and drug resistance, there is a lack of an extensive study on how the deleterious non-synonymous SNPs (nsSNPs) disrupt its phenotypic effects. In this study, we aim at discovering the structural and functional consequences of nsSNPs in DHFR by employing a combined computational approach consisting of ten recently developed in silico tools for identification of damaging nsSNPs and molecular dynamics (MD) simulation for getting deeper insights into the magnitudes of damaging effects. Our study revealed the presence of 12 most deleterious nsSNPs affecting the native phenotypic effects, with three (R71T, G118D, Y122D) identified in the co-factor and ligand binding active sites. MD simulations also suggested that these three SNPs particularly Y122D, alter the overall structural flexibility and dynamics of the native DHFR protein which can provide more understandings into the crucial roles of these mutants in influencing the loss of DHFR function.
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Affiliation(s)
- Md Shahed Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Abu Saleh
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Ashik Tanvir Riham
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Selangor Darul Ehsan, Malaysia
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King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci 2021; 8:712085. [PMID: 34458321 PMCID: PMC8387144 DOI: 10.3389/fmolb.2021.712085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/11/2023] Open
Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
- Department of Materials Science and Engineering, University of California, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
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Schiliro C, Firestein BL. Mechanisms of Metabolic Reprogramming in Cancer Cells Supporting Enhanced Growth and Proliferation. Cells 2021; 10:cells10051056. [PMID: 33946927 PMCID: PMC8146072 DOI: 10.3390/cells10051056] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer cells alter metabolic processes to sustain their characteristic uncontrolled growth and proliferation. These metabolic alterations include (1) a shift from oxidative phosphorylation to aerobic glycolysis to support the increased need for ATP, (2) increased glutaminolysis for NADPH regeneration, (3) altered flux through the pentose phosphate pathway and the tricarboxylic acid cycle for macromolecule generation, (4) increased lipid uptake, lipogenesis, and cholesterol synthesis, (5) upregulation of one-carbon metabolism for the production of ATP, NADH/NADPH, nucleotides, and glutathione, (6) altered amino acid metabolism, (7) metabolism-based regulation of apoptosis, and (8) the utilization of alternative substrates, such as lactate and acetate. Altered metabolic flux in cancer is controlled by tumor-host cell interactions, key oncogenes, tumor suppressors, and other regulatory molecules, including non-coding RNAs. Changes to metabolic pathways in cancer are dynamic, exhibit plasticity, and are often dependent on the type of tumor and the tumor microenvironment, leading in a shift of thought from the Warburg Effect and the “reverse Warburg Effect” to metabolic plasticity. Understanding the complex nature of altered flux through these multiple pathways in cancer cells can support the development of new therapies.
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Affiliation(s)
- Chelsea Schiliro
- Cell and Developmental Biology Graduate Program and Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA;
| | - Bonnie L. Firestein
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA
- Correspondence: ; Tel.: +1-848-445-8045
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Parate S, Kumar V, Lee G, Rampogu S, Hong JC, Lee KW. Marine-Derived Natural Products as ATP-Competitive mTOR Kinase Inhibitors for Cancer Therapeutics. Pharmaceuticals (Basel) 2021; 14:ph14030282. [PMID: 33801030 PMCID: PMC8003863 DOI: 10.3390/ph14030282] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 02/08/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) is a serine/threonine kinase portraying a quintessential role in cellular proliferation and survival. Aberrations in the mTOR signaling pathway have been reported in numerous cancers including thyroid, lung, gastric and ovarian cancer, thus making it a therapeutic target. To attain this objective, an in silico investigation was designed, employing a pharmacophore modeling approach. A structure-based pharmacophore (SBP) model exploiting the key features of a selective mTOR inhibitor, Torkinib directed at the ATP-binding pocket was generated. A Marine Natural Products (MNP) library was screened using SBP model as a query. The retrieved compounds after consequent drug-likeness filtration were subjected to molecular docking with mTOR, thus revealing four MNPs with better scores than Torkinib. Successive refinement via molecular dynamics simulations demonstrated that the hits formed crucial interactions with key residues of the pocket. Furthermore, the four identified hits exhibited good binding free energy scores through MM-PBSA calculations and the subsequent in silico toxicity assessments displayed three hits deemed essentially non-carcinogenic and non-mutagenic. The hits presented in this investigation could act as potent ATP-competitive mTOR inhibitors, representing a platform for the future discovery of drugs from marine natural origin.
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Affiliation(s)
- Shraddha Parate
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Vikas Kumar
- Division of Life Sciences, Department of Bio & Medical Big Data (BK21 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (V.K.); (S.R.)
| | - Gihwan Lee
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
| | - Shailima Rampogu
- Division of Life Sciences, Department of Bio & Medical Big Data (BK21 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (V.K.); (S.R.)
| | - Jong Chan Hong
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.P.); (G.L.)
- Correspondence: (J.C.H.); (K.W.L.); Tel.: +82-55-772-1360 (K.W.L.)
| | - Keun Woo Lee
- Division of Life Sciences, Department of Bio & Medical Big Data (BK21 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (V.K.); (S.R.)
- Correspondence: (J.C.H.); (K.W.L.); Tel.: +82-55-772-1360 (K.W.L.)
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Feng C, Chen R, Wang K, Wen C, Xu Z. Chinese traditional medicine (GuiZhi-ShaoYao-ZhiMu decoction) as an add-on medication to methotrexate for rheumatoid arthritis: a meta-analysis of randomized clinical trials. Ther Adv Chronic Dis 2021; 12:2040622321993438. [PMID: 33633825 PMCID: PMC7887670 DOI: 10.1177/2040622321993438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 01/15/2021] [Indexed: 12/23/2022] Open
Abstract
Background GuiZhi-ShaoYao-ZhiMu decoction (GSZD), a traditional Chinese herbal medication, has been frequently used as an add-on medication to methotrexate (MTX) for rheumatoid arthritis (RA) treatment in China. This meta-analysis evaluated the efficacy and safety of adding GSZD to MTX for RA treatment. Methods We performed a systematic search of PubMed, Web of Science, EMBASE, and the Cochrane Library (all databases) for English-language studies and WanFang, VIP, and CNKI for Chinese-language studies up to 28 July 2020. Data from selected studies, mainly the response rates and rate of adverse events (AEs), were extracted independently by two authors, and a random-effects model (Mantel-Haenszel method) was used for the meta-analysis. Results A total of 14 randomized controlled trials and 1224 patients were included (623 patients in the GSZD + MTX group and 601 patients in the MTX group). For efficacy, the meta-analysis found that combining GSZD with MTX increased the effective rate [relative risk (RR) = 1.24, 95% confidence interval (CI): 1.18-1.30, based on 1069 patients], defined as >30% efficacy, American College of Rheumatology 20, or a decrease of disease activity score 28 >0.6. Adding GSZD reduced the swollen and tender joint counts, the duration of morning stiffness, the levels of C-reactive protein and rheumatoid factor, and erythrocyte sedimentation rate. The adjuvant therapeutic effect of GSZD was independent of the dose of MTX or the combined utilization of other drugs in both groups. For safety, adding GSZD was associated with a lower rate of total AEs (RR = 0.46, 95% CI: 0.26-0.83, based on 615 patients) and gastrointestinal tract AEs (RR = 0.46, 95% CI: 0.24-0.88, based on 537 patients). Conclusion Combining GSZD with MTX may be a more efficacious and safer strategy for treating RA compared with MTX alone. Further large studies are warranted to investigate the long-term efficacy and safety of adding GSZD to MTX for RA treatment.
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Affiliation(s)
- Chenxi Feng
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Rongrong Chen
- School of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Keer Wang
- School of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Chengping Wen
- School of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Zhenghao Xu
- School of Basic Medical Science, Zhejiang Chinese Medical University, Binwen Road 548, Hangzhou, Zhejiang, 310053, China
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