1
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Sabbah DA, Hajjo R, Bardaweel SK, Zhong HA. Targeting the PI3K/AKT signaling pathway in anticancer research: a recent update on inhibitor design and clinical trials (2020-2023). Expert Opin Ther Pat 2024; 34:141-158. [PMID: 38557273 DOI: 10.1080/13543776.2024.2338100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Recent years have witnessed great achievements in drug design and development targeting the phosphatidylinositol 3-kinase/protein kinase-B (PI3K/AKT) signaling pathway, a pathway central to cell growth and proliferation. The nearest neighbor protein-protein interaction networks for PI3K and AKT show the interplays between these target proteins which can be harnessed for drug discovery. In this review, we discuss the drug design and clinical development of inhibitors of PI3K/AKT in the past three years. We review in detail the structures, selectivity, efficacy, and combination therapy of 35 inhibitors targeting these proteins, classified based on the target proteins. Approaches to overcoming drug resistance and to minimizing toxicities are discussed. Future research directions for developing combinational therapy and PROTACs of PI3K and AKT inhibitors are also discussed. AREA COVERED This review covers clinical trial reports and patent literature on inhibitors of PI3K and AKT published between 2020 and 2023. EXPERT OPINION To address drug resistance and drug toxicity of inhibitors of PI3K and AKT, it is highly desirable to design and develop subtype-selective PI3K inhibitors or subtype-selective AKT1 inhibitors to minimize toxicity or to develop allosteric drugs that can form covalent bonds. The development of PROTACs of PI3Kα or AKT helps to reduce off-target toxicities.
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Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- National Center for Epidemics and Communicable Disease Control (JCDC), Amman, Jordan
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman, Jordan
| | - Haizhen A Zhong
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, Omaha, NE, USA
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2
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Al Hasan M, Sabirianov M, Redwine G, Goettsch K, Yang SX, Zhong HA. Binding and selectivity studies of phosphatidylinositol 3-kinase (PI3K) inhibitors. J Mol Graph Model 2023; 121:108433. [PMID: 36812742 DOI: 10.1016/j.jmgm.2023.108433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Overexpression of the Phosphatidylinositol 3-kinase (PI3K) proteins have been observed in cancer cells. Targeting the phosphatidylinositol 3-kinase (PI3K) signaling transduction pathway by inhibition of the PI3K substrate recognition sites has been proved to be an effective approach to block cancer progression. Many PI3K inhibitors have been developed. Seven drugs have been approved by the US FDA with a mechanism of targeting the phosphatidylinositol 3-kinase/protein kinase-B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway. In this study, we used docking tools to investigate selective binding of ligands toward four different subtypes of PI3Ks (PI3Kα, PI3Kβ, PI3Kγ and PI3Kδ). The affinity predicted from both the Glide dock and the Movable-Type (MT)-based free energy calculations agreed well with the experimental data. The validation of our predicted methods with a large dataset of 147 ligands showed very small mean errors. We identified residues that may dictate the subtype-specific binding. Particularly, residues Asp964, Ser806, Lys890 and Thr886 of PI3Kγ might be utilized for PI3Kγ-selective inhibitor design. Residues Val828, Trp760, Glu826 and Tyr813 may be important for PI3Kδ-selective inhibitor binding.
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Affiliation(s)
- Mohammad Al Hasan
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Matthew Sabirianov
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Grace Redwine
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Kaitlin Goettsch
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Stephen X Yang
- Westlake High School, 100 Lakeview Canyon Rd, Thousand Oaks, CA, 91362, USA
| | - Haizhen A Zhong
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA.
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Fındık V, Varınca Gerçik BT, Sinek Ö, Erdem SS, Ruiz-López MF. Mechanistic Investigation of Lysine-Targeted Covalent Inhibition of PI3Kδ via ONIOM QM:QM Computations. J Chem Inf Model 2022; 62:6775-6787. [PMID: 35980989 DOI: 10.1021/acs.jcim.2c00569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) enzymes are important drug targets, especially in oncology, and several inhibitors are currently under investigation in clinical trials for the treatment of lymphocytic leukemia, follicular lymphoma, breast, thyroid, colorectal, and lung cancer. Targeted covalent inhibitors hold significant promise for drug discovery research especially for kinases. Targeting the lysine residues attracts attention as a new strategy in designing targeted covalent inhibitors, since the lysine residue provides several advantages over the traditional cysteine residue. Recently, new highly selective covalent inhibitors of PI3Kδ with activated ester warheads, targeting the conserved Lys779 residue, were reported. Based on the observed kinetics, a covalent inhibition mechanism was proposed, but the atomistic details of the reaction are still not understood. Therefore, in the present work, we have conducted quantum chemical ONIOM M06-2X/6-31+G(d,p):PM6 calculations on the active site cluster structure of PI3Kδ to elucidate the microscopic details of the mechanism of the aminolysis reaction between Lys779 and the ester inhibitors. Our calculations clearly discriminate the noncovalent methyl ester inhibitor and the covalent inhibitors with activated phenolic esters. For the representative p-NO2, p-F, p-H, and p-OCH3 phenolic esters, the Gibbs free energy profiles of alternative mechanistic paths through either Asp782 or Asp911 demonstrate the modulatory role of active site aspartate residues. The most plausible path alters depending on the electron-withdrawing/donating nature of the p-substituted phenolate leaving group. Inhibitors with sufficiently strong electron-withdrawing group prefer direct dissociation of the leaving group from the tetrahedral zwitterion intermediate, while the ones with electron-donating group favor the formation of a neutral tetrahedral intermediate prior to the dissociation. The relative Gibbs free energy barriers of p-NO2 < p-F < p-H < p-OCH3 substituted phenyl esters display the same qualitative trend as the experimentally measured kinact/KI values. Our results provide in depth insight into the mechanism, which can pave the way for optimizing the inhibitor efficiency.
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Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, 54000, Nancy, France.,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | | | - Öykü Sinek
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
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Sweidan K, Elfadel H, Sabbah DA, Bardaweel SK, Hajjo R, Anjum S, Sinoj J, Nair VA, Abu‐Gharbieh E, El‐Huneidi W. Novel Derivatives of 4,6‐Dihydroxy‐2‐Quinolone‐3‐Carboxamides as Potential PI3Kα Inhibitors. ChemistrySelect 2022. [DOI: 10.1002/slct.202202263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kamal Sweidan
- Department of Chemistry Institution The University of Jordan Amman 11942 Jordan
| | - Hussein Elfadel
- Department of Chemistry Institution The University of Jordan Amman 11942 Jordan
| | - Dima A. Sabbah
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan P.O. Box 130 Amman 11733 Jordan
| | - Sanaa K. Bardaweel
- Department of Pharmaceutical Sciences School of Pharmacy Institution The University of Jordan Amman 11942 Jordan
| | - Rima Hajjo
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan P.O. Box 130 Amman 11733 Jordan
| | - Shabana Anjum
- Sharjah Institute for Medical Research Institution University of Sharjah Sharjah 27272 United Arab Emirates
| | - Jithna Sinoj
- Sharjah Institute for Medical Research Institution University of Sharjah Sharjah 27272 United Arab Emirates
| | - Vidhya A. Nair
- Sharjah Institute for Medical Research Institution University of Sharjah Sharjah 27272 United Arab Emirates
| | - Eman Abu‐Gharbieh
- Sharjah Institute for Medical Research Institution University of Sharjah Sharjah 27272 United Arab Emirates
- College of Medicine Institution University of Sharjah Sharjah 27272 United Arab Emirates
| | - Waseem El‐Huneidi
- Sharjah Institute for Medical Research Institution University of Sharjah Sharjah 27272 United Arab Emirates
- College of Medicine Institution University of Sharjah Sharjah 27272 United Arab Emirates
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Sabbah DA, Samarat HH, Al‐Shalabi E, Bardaweel SK, Hajjo R, Sweidan K, Khalaf RA, Al‐Zuheiri AM, Abushaikha G. Design, Synthesis, and Biological Examination of
N‐
Phenyl‐6‐fluoro‐4‐hydroxy‐2‐quinolone‐3‐carboxamides as Anticancer Agents. ChemistrySelect 2022. [DOI: 10.1002/slct.202200662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dima A. Sabbah
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan Address P.O. Box 130 Amman 11733 Jordan
| | - Hla H. Samarat
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan Address P.O. Box 130 Amman 11733 Jordan
| | - Eveen Al‐Shalabi
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan Address P.O. Box 130 Amman 11733 Jordan
| | - Sanaa K. Bardaweel
- Department of Pharmaceutical Sciences School of Pharmacy Institution The University of Jordan Address Amman 11942 Jordan
| | - Rima Hajjo
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan Address P.O. Box 130 Amman 11733 Jordan
- Laboratory for Molecular Modeling Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy The University of North Carlina at Chapel Hill Chapel Hill NC 27515 USA
| | - Kamal Sweidan
- Department of Chemistry Institution The University of Jordan Address Amman 11942 Jordan
| | - Reema Abu Khalaf
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan Address P.O. Box 130 Amman 11733 Jordan
| | - Aya M. Al‐Zuheiri
- Department of Pharmacy Faculty of Pharmacy Institution Al-Zaytoonah University of Jordan Address P.O. Box 130 Amman 11733 Jordan
| | - Ghassan Abushaikha
- Department of Medicinal and Biological Chemistry College of Pharmacy and Pharmaceutical Sciences Institution The University of Toledo Address Toledo OH 43606-3390 USA
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Bhaskar BV, Rammohan A, Babu TM, Zheng GY, Chen W, Rajendra W, Zyryanov GV, Gu W. Molecular insight into isoform specific inhibition of PI3K-α and PKC-η with dietary agents through an ensemble pharmacophore and docking studies. Sci Rep 2021; 11:12150. [PMID: 34108504 PMCID: PMC8190100 DOI: 10.1038/s41598-021-90287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023] Open
Abstract
Dietary compounds play an important role in the prevention and treatment of many cancers, although their specific molecular mechanism is not yet known. In the present study, thirty dietary agents were analyzed on nine drug targets through in silico studies. However, nine dietary scaffolds, such as silibinin, flavopiridol, oleandrin, ursolic acid, α-boswellic acid, β-boswellic acid, triterpenoid, guggulsterone, and oleanolic acid potentially bound to the cavity of PI3K-α, PKC-η, H-Ras, and Ras with the highest binding energy. Particularly, the compounds silibinin and flavopiridol have been shown to have broad spectrum anticancer activity. Interestingly, flavopiridol was embedded in the pockets of PI3K-α and PKC-η as bound crystal inhibitors in two different conformations and showed significant interactions with ATP binding pocket residues. However, complex-based pharmacophore modeling achieved two vital pharmacophoric features namely, two H-bond acceptors for PI3K-α, while three are hydrophobic, one cat-donor and one H-bond donor and acceptor for PKC-η, respectively. The database screening with the ChemBridge core library explored potential hits on a valid pharmacophore query. Therefore, to optimize perspective lead compounds from the hits, which were subjected to various constraints such as docking, MM/GBVI, Lipinski rule of five, ADMET and toxicity properties. Henceforth, the top ligands were sorted out and examined for vital interactions with key residues, arguably the top three promising lead compounds for PI3K-α, while seven for PKC-η, exhibiting binding energy from - 11.5 to - 8.5 kcal mol-1. Therefore, these scaffolds could be helpful in the development of novel class of effective anticancer agents.
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Affiliation(s)
- Baki Vijaya Bhaskar
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China.
| | - Aluru Rammohan
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Ekaterinburg, 620002, Russia
| | | | - Gui Yu Zheng
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China
| | - Weibin Chen
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China
| | - Wudayagiri Rajendra
- Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, 517502, India
| | - Grigory V Zyryanov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Ekaterinburg, 620002, Russia
| | - Wei Gu
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China.
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Sabbah DA, Hajjo R, Bardaweel SK, Zhong HA. Phosphatidylinositol 3-kinase (PI3K) inhibitors: a recent update on inhibitor design and clinical trials (2016-2020). Expert Opin Ther Pat 2021; 31:877-892. [PMID: 33970742 DOI: 10.1080/13543776.2021.1924150] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: The phosphatidylinositol 3-kinase/protein kinase-B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway plays a central role in regulating cell growth and proliferation and thus has been considered as effective anticancer drug targets. Many PI3K inhibitors have been developed and progressed to various stages of clinical trials, and some have been approved as anticancer treatment. In this review, we discuss the drug design and clinical development of PI3K inhibitors over the past 4 years. We review the selectivity and potency of 47 PI3K inhibitors. Structural determinants for increasing selectivity toward PI3K subtype-selectivity or mutant selectivity are discussed. Future research direction and current clinical development in combination therapy of inhibitors involved in PI3Ks are also discussed.Area covered: This review covers clinical trial reports and patent literature on PI3K inhibitors and their selectivity published between 2016 and 2020.Expert opinion: To PI3Kα mutants (E542K, E545K, and H1047R), it is highly desirable to design and develop mutant-specific PI3K inhibitors. It is also necessary to develop subtype-selective PI3Kα inhibitors to minimize toxicity. To reduce drug resistance and to improve efficacy, future studies should include combination therapy of PI3K inhibitors with existing anticancer drugs from different pathways.
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Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman, Jordan
| | - Haizhen A Zhong
- DSC 362, Department of Chemistry, The University of Nebraska at Omaha, Omaha, Nebraska, USA
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Bilginer S, Bardaweel SK, Sabbah DA, Gul HI. Docking Studies and Antiproliferative Activities of 6-(3-aryl-2-propenoyl)-2(3H)- benzoxazolone Derivatives as Novel Inhibitors of Phosphatidylinositol 3-Kinase (PI3Kα). Anticancer Agents Med Chem 2021; 21:716-724. [PMID: 32767959 DOI: 10.2174/1871520620666200807221731] [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: 04/10/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cancer is a life-threatening group of diseases and universally, the second main cause of death. The design and development of new scaffolds targeting selective cancer cells are considered a promising goal for cancer treatment. AIMS AND OBJECTIVE Chalcone derivatives; 6-(3-aryl-2-propenoyl)-2(3H)-benzoxazolone, were previously prepared and evaluated against the oral cavity squamous cell carcinoma cell line, HSC-2, and were reported to have remarkably high tumor selectivity. The aim of this study was to further investigate the anticancer activities of the chalcone derivatives against human colon cancer cells with a possible elucidation of their mechanism of action. METHODS Computational studies were conducted to explore the potential interaction of the synthesized molecules with the phosphatidylinositol-4,5-bisphosphate 3-kinaseα (PI3Kα). Biological evaluation of the antiproliferative activities associated with compounds 1-23 was carried out against the colon cancer cell line, HCT116. Lactate Dehydrogenase (LDH) activity was measured to study necrosis, while the caspase-3 activation and DNA measurements were used to evaluate apoptosis in the treated cells. RESULTS Glide studies against PI3Kα kinase domain demonstrated that the 6-(3-aryl-2-propenoyl)-2(3H)- benzoxazolone scaffold forms H-bond with K802, Y836, E849, V851, N853, Q859, and D933, and it fits the fingerprint of PI3Kα active inhibitors. Biological evaluation of the reported compounds in HCT116 cell line confirmed that the series inhibited PI3Kα activity and induced apoptosis via activation of caspase-3 and reduction of DNA content. CONCLUSION The recently developed compounds might be employed as lead structures for the design of new antitumor drugs targeting PI3Kα.
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Affiliation(s)
- Sinan Bilginer
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ataturk University, Erzurum, Turkey
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman 11733, Jordan
| | - Halise Inci Gul
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ataturk University, Erzurum, Turkey
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N-Phenyl-6-Chloro-4-Hydroxy-2-Quinolone-3-CarboxAmides: Molecular Docking, Synthesis, and Biological Investigation as Anticancer Agents. Molecules 2020; 26:molecules26010073. [PMID: 33375766 PMCID: PMC7795513 DOI: 10.3390/molecules26010073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is a multifactorial disease and the second leading cause of death worldwide. Diverse factors induce carcinogenesis, such as diet, smoking, radiation, and genetic defects. The phosphatidylinositol 3-kinase (PI3Kα) has emerged as an attractive target for anticancer drug design. Eighteen derivatives of N-phenyl-6-chloro-4-hydroxy-2-quinolone-3-carboxamide were synthesized and characterized using FT-IR, NMR (1H and 13C), and high-resolution mass spectra (HRMS). The series exhibited distinct antiproliferative activity (IC50 µM) against human epithelial colorectal adenocarcinoma (Caco-2) and colon carcinoma (HCT-116) cell lines, respectively: compounds 16 (37.4, 8.9 µM), 18 (50.9, 3.3 µM), 19 (17.0, 5.3 µM), and 21 (18.9, 4.9 µM). The induced-fit docking (IFD) studies against PI3Kαs showed that the derivatives occupy the PI3Kα binding site and engage with key binding residues.
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Sabbah DA, Hasan SE, Abu Khalaf R, Bardaweel SK, Hajjo R, Alqaisi KM, Sweidan KA, Al-Zuheiri AM. Molecular Modeling, Synthesis and Biological Evaluation of N-Phenyl-4-Hydroxy-6-Methyl-2-Quinolone-3-CarboxAmides as Anticancer Agents. Molecules 2020; 25:molecules25225348. [PMID: 33207767 PMCID: PMC7698136 DOI: 10.3390/molecules25225348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/22/2023] Open
Abstract
The emergence of phosphatidylinositol 3-kinase (PI3Kα) in cancer development has accentuated its significance as a potential target for anticancer drug design. Twenty one derivatives of N-phenyl-4-hydroxy-6-methyl-2-quinolone-3-carboxamide were synthesized and characterized using NMR (1H and 13C) and HRMS. The derivatives displayed inhibitory activity against human epithelial colorectal adenocarcinoma (Caco-2) and human colon cancer (HCT-116) cell lines: compounds 8 (IC50 Caco-2 = 98 µM, IC50 HCT-116 = 337 µM) and 16 (IC50 Caco-2 = 13 µM, IC50 HCT-116 = 240.2 µM). Results showed that compound 16 significantly affected the gene encoding AKT, BAD, and PI3K. The induced-fit docking (IFD) studies against PI3Kα demonstrated that the scaffold accommodates the kinase domains and forms H-bonds with significant binding residues.
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Affiliation(s)
- Dima A. Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan; (S.E.H.); (R.A.K.); (R.H.); (A.M.A.-Z.)
- Correspondence: ; Tel.: +962-6429-1511
| | - Shaima’ E. Hasan
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan; (S.E.H.); (R.A.K.); (R.H.); (A.M.A.-Z.)
| | - Reema Abu Khalaf
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan; (S.E.H.); (R.A.K.); (R.H.); (A.M.A.-Z.)
| | - Sanaa K. Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman 11942, Jordan;
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan; (S.E.H.); (R.A.K.); (R.H.); (A.M.A.-Z.)
| | - Khalid M. Alqaisi
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman 19328, Jordan;
- Pharmacological and Diagnostic Research Centre (PDRC), Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 19328, Jordan
| | - Kamal A. Sweidan
- Department of Chemistry, The University of Jordan, Amman 11942, Jordan;
| | - Aya M. Al-Zuheiri
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan; (S.E.H.); (R.A.K.); (R.H.); (A.M.A.-Z.)
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Zhu J, Ke K, Xu L, Jin J. Theoretical studies on the selectivity mechanisms of PI3Kδ inhibition with marketed idelalisib and its derivatives by 3D-QSAR, molecular docking, and molecular dynamics simulation. J Mol Model 2019; 25:242. [DOI: 10.1007/s00894-019-4129-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/09/2019] [Indexed: 01/01/2023]
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Zhu J, Ke K, Xu L, Jin J. Discovery of a novel phosphoinositide 3-kinase gamma (PI3Kγ) inhibitor against hematologic malignancies and theoretical studies on its PI3Kγ-specific binding mechanisms. RSC Adv 2019; 9:20207-20215. [PMID: 35546906 PMCID: PMC9087882 DOI: 10.1039/c9ra02649e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/24/2019] [Indexed: 12/28/2022] Open
Abstract
Class IB phosphoinositide 3-kinase gamma (PI3Kγ) is vital for regulating intracellular signaling pathways and has become an attractive drug target for the treatment of malignant tumors. In the present study, one potent PI3Kγ inhibitor (JN-PK1) with a novel scaffold against hematologic malignancies was identified based on a series of biological experiments, and then the selective mechanism of PI3Kγ inhibition was explored by a systematic computational method. JN-PK1 shows an effective antiproliferative activity on several cancer cell lines, especially blood cancer cells. Cell-free enzymatic studies demonstrated that JN-PK1 specifically inhibits PI3Kγ at low micromolar concentrations without affecting other isoforms of PI3K. In the cellular context, JN-PK1 potently inhibits PI3K/Akt/mTOR signaling pathway in a time- and concentration-dependent manner, which leads to the apoptosis of cancer cells. Further, the specific binding mode of JN-PK1 with PI3Kγ was illustrated by molecular docking, and the selective inhibition mechanism of PI3Kγ by JN-PK1 was revealed by molecular dynamics simulation. Finally, some key residues of PI3Kγ required for specificity and activity were identified. Taken together, JN-PK1 may be developed as a promising therapeutic agent for the treatment of hematologic malignancies.
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Affiliation(s)
- Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University Wuxi Jiangsu 214122 China
| | - Ke Ke
- School of Pharmaceutical Sciences, Jiangnan University Wuxi Jiangsu 214122 China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology Changzhou 213001 China
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University Wuxi Jiangsu 214122 China
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Sabbah DA, Ibrahim AH, Talib WH, Alqaisi KM, Sweidan K, Bardaweel SK, Sheikha GA, Zhong HA, Al-Shalabi E, Khalaf RA, Mubarak MS. Ligand-Based Drug Design: Synthesis and Biological Evaluation of Substituted Benzoin Derivatives as Potential Antitumor Agents. Med Chem 2019; 15:417-429. [DOI: 10.2174/1573406414666180912111846] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/02/2018] [Accepted: 09/10/2018] [Indexed: 11/22/2022]
Abstract
Background:
Phosphoinositide 3-kinase α (PI3Kα) has emerged as a promising target
for anticancer drug design.
Objectives:
Target compounds were designed to investigate the effect of the p-OCH3 motifs on
ligand/PI3Kα complex interaction and antiproliferative activity.
Methods:
Synthesis of the proposed compounds, biological examination tests against human colon
adenocarcinoma (HCT-116), breast adenocarcinoma (MCF-7), and breast carcinoma (T47D) cell
lines, along with Glide docking studies.
Results:
A series of 1,2-bis(4-methoxyphenyl)-2-oxoethyl benzoates was synthesized and characterized
by means of FT-IR, 1H and 13C NMR, and by elemental analysis. Biological investigation
demonstrated that the newly synthesized compounds exhibit antiproliferative activity in human colon
adenocarcinoma (HCT-116), breast adenocarcinoma (MCF-7), and breast carcinoma (T47D)
cell lines possibly via inhibition of PI3Kα and estrogen receptor alpha (ERα). Additionally, results
revealed that these compounds exert selective inhibitory activity, induce apoptosis, and suppress
VEGF production. Compound 3c exhibited promising antiproliferative activity in HCT-116 interrogating
that hydrogen bond-acceptor mediates ligand/PI3Kα complex formation on m- position.
Compounds 3e and 3i displayed high inhibitory activity in MCF-7 and T47D implying a wide cleft
discloses the o-attachment. Furthermore, compound 3g exerted selective inhibitory activity against
T47D. Glide docking studies against PI3Kα and ERα demonstrated that the series accommodate
binding to PI3Kα and/or ERα.
Conclusion:
The series exhibited a potential antitumor activity in human carcinoma cell lines encoding
PI3Kα and/or ERα.
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Affiliation(s)
- Dima A. Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130 Amman 11733, Jordan
| | - Ameerah H. Ibrahim
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130 Amman 11733, Jordan
| | - Wamidh H. Talib
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman, Jordan
| | - Khalid M. Alqaisi
- Department of Allied Medical Sciences, Zarqa University College, Al-Balqa Applied University, P.O. Box 132222, Zarqa 13132, Jordan
| | - Kamal Sweidan
- Department of Chemistry, The University of Jordan, Amman 11942, Jordan
| | - Sanaa K. Bardaweel
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Ghassan A. Sheikha
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130 Amman 11733, Jordan
| | - Haizhen A. Zhong
- DSC 362, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182, United States
| | - Eveen Al-Shalabi
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130 Amman 11733, Jordan
| | - Reema A. Khalaf
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130 Amman 11733, Jordan
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14
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Mahmoud N, Sabbah DA, Abu-Dahab R, Abuarqoub D, Abdallah M, (Hasan Ibrahim) A, Khalil EA. Cholesterol-coated gold nanorods as an efficient nano-carrier for chemotherapeutic delivery and potential treatment of breast cancer: in vitro studies using the MCF-7 cell line. RSC Adv 2019; 9:12718-12731. [PMID: 35515852 PMCID: PMC9063807 DOI: 10.1039/c9ra01041f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/10/2019] [Indexed: 01/15/2023] Open
Abstract
Gold nanorods (GNRs) have a recognized role in treatment of cancers as efficient nanocarriers for chemotherapeutic drug delivery. In this study, GNRs modified with cholesterol-PEG were employed as a nanocarrier for a hydrophobic compound having a promising phosphatidylinositol 3-kinase (PI3Kα) inhibitory activity. The acquired nanocomplex was characterized by optical and infra-red (IR) absorption spectroscopies, in addition to hydrodynamic size and zeta potential. Glide docking and superposing of docked poses of the hydrophobic ligand and cholesterol moiety demonstrated that hydrophobic interactions drive the conjugation and attachment of the ligand to the cholesterol moiety of the nanocarrier. In vitro release study under a cellular environment indicates that the presence of cells has enhanced the release and the cellular uptake of the conjugated ligand. Furthermore, the anti-proliferative assay of the nanocomplex revealed potent cytotoxicity over a low concentration range of the nanocomplex against MCF-7 breast cancer cells compared to the free compound or the nanocarrier alone. Analysis of cellular death modality by flow cytometry showed that the nanocomplex has a rapid effect on cell death, as cells went toward the late apoptotic/necrotic stage rapidly and proportionally to the increase of the nanocomplex concentration. The overall results propose that cholesterol-decorated GNRs could be considered as a promising nanocarrier for hydrophobic drugs to achieve efficient delivery and potential therapy against breast cancer cells. Gold nanorods demonstrate a recognized role in the treatment of breast cancer cell lines as an efficient nanocarrier for chemotherapeutic drug delivery.![]()
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Affiliation(s)
- Nouf N. Mahmoud
- Faculty of Pharmacy
- Al-Zaytoonah University of Jordan
- Amman 11733
- Jordan
| | - Dima A. Sabbah
- Faculty of Pharmacy
- Al-Zaytoonah University of Jordan
- Amman 11733
- Jordan
| | - Rana Abu-Dahab
- School of Pharmacy
- The University of Jordan
- Amman 11942
- Jordan
| | - Duaa Abuarqoub
- Cell Therapy Center
- The University of Jordan
- Amman 11942
- Jordan
| | - Maha Abdallah
- School of Pharmacy
- The University of Jordan
- Amman 11942
- Jordan
| | | | - Enam A. Khalil
- School of Pharmacy
- The University of Jordan
- Amman 11942
- Jordan
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15
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Al-Blewi FF, Rezki N, Al-Sodies SA, Bardaweel SK, Sabbah DA, Messali M, Aouad MR. Novel amphiphilic pyridinium ionic liquids-supported Schiff bases: ultrasound assisted synthesis, molecular docking and anticancer evaluation. Chem Cent J 2018; 12:118. [PMID: 30467608 PMCID: PMC6768046 DOI: 10.1186/s13065-018-0489-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/13/2018] [Indexed: 11/15/2022] Open
Abstract
Background Pyridinium Schiff bases and ionic liquids have attracted increasing interest in medicinal chemistry. Results A library of 32 cationic fluorinated pyridinium hydrazone-based amphiphiles tethering fluorinated counteranions was synthesized by alkylation of 4-fluoropyridine hydrazone with various long alkyl iodide exploiting lead quaternization and metathesis strategies. All compounds were assessed for their anticancer inhibition activity towards different cancer cell lines and the results revealed that increasing the length of the hydrophobic chain of the synthesized analogues appears to significantly enhance their anticancer activities. Substantial increase in caspase-3 activity was demonstrated upon treatment with the most potent compounds, namely 8, 28, 29 and 32 suggesting an apoptotic cellular death pathway. Conclusions Quantum-polarized ligand docking studies against phosphoinositide 3-kinase α displayed that compounds 2–6 bind to the kinase site and form H-bond with S774, K802, H917 and D933. ![]() Electronic supplementary material The online version of this article (10.1186/s13065-018-0489-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fawzia Faleh Al-Blewi
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah, Medina, 30002, Saudi Arabia
| | - Nadjet Rezki
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah, Medina, 30002, Saudi Arabia. .,Department of Chemistry, Faculty of Sciences, University of Sciences and Technology Mohamed Boudiaf, Laboratoire de Chimie et Electrochimie des Complexes Metalliques (LCECM) USTO-MB, P.O. Box 1505, El M'nouar, 31000, Oran, Algeria.
| | - Salsabeel Abdullah Al-Sodies
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah, Medina, 30002, Saudi Arabia
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, 11942, Jordan
| | - Dima A Sabbah
- Faculty of Pharmacy, Al-Zaytoonah University, Amman, 11733, Jordan
| | - Mouslim Messali
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah, Medina, 30002, Saudi Arabia
| | - Mohamed Reda Aouad
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah, Medina, 30002, Saudi Arabia.
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16
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Jin X, Kwon W, Kim TS, Heo JN, Chung HC, Choi J, No KT. Identification of Natural Products as Novel PI3Kβ Inhibitors Through Pharmacophore-based Virtual Screening. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xuemei Jin
- Department of Biotechnology; Yonsei University; Seoul 03722 Korea
| | - Woosun Kwon
- Song-Dang Institute for Cancer Research; Cancer Metastasis Research Center, Yonsei University College of Medicine; Seoul 03722 Korea
| | - Tae Soo Kim
- Song-Dang Institute for Cancer Research; Cancer Metastasis Research Center, Yonsei University College of Medicine; Seoul 03722 Korea
| | - Jung-Nyoung Heo
- Korea Research Institute of Chemical Technology; Daejeon 34114 Republic of Korea
| | - Hyun Cheol Chung
- Song-Dang Institute for Cancer Research; Cancer Metastasis Research Center, Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine; Seoul 03722 Korea
| | - Jiwon Choi
- Bioinformatics & Molecular Design Research Center (BMDRC); Yonsei University; Seoul 03722 Korea
| | - Kyoung Tai No
- Department of Biotechnology; Yonsei University; Seoul 03722 Korea
- Bioinformatics & Molecular Design Research Center (BMDRC); Yonsei University; Seoul 03722 Korea
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17
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Yan L, Zhang L, Zhang Y, Qiao X, Pan J, Liu H, Lu S, Xiang B, Lu T, Yuan H. Insight into the key features for ligand binding in Y1230 mutated c-Met kinase domain by molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:2015-2031. [DOI: 10.1080/07391102.2017.1340852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Libo Yan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Li Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Yanmin Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Xin Qiao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Jing Pan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Haichun Liu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Shuai Lu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Bingren Xiang
- Center for instrument analysis, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Tao Lu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
| | - Haoliang Yuan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P.R. China
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18
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Selvaraj C, Krishnasamy G, Jagtap SS, Patel SK, Dhiman SS, Kim TS, Singh SK, Lee JK. Structural insights into the binding mode of d-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α. Molecules 2016; 21:molecules21070857. [PMID: 27367663 PMCID: PMC6274547 DOI: 10.3390/molecules21070857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/23/2016] [Accepted: 06/23/2016] [Indexed: 11/16/2022] Open
Abstract
Phosphatidylinositol 3-kinase α (PI3Kα) is an attractive target for anticancer drug design. Liphagal, isolated from the marine sponge Aka coralliphaga, possesses the special “liphagane” meroterpenoid carbon skeleton and has been demonstrated as a PI3Kα inhibitor. Molecular docking and molecular dynamics simulations were performed to explore the dynamic behaviors of PI3Kα binding with liphagal, and free energy calculations and energy decomposition analysis were carried out by use of molecular mechanics/Poisson-Boltzmann (generalized Born) surface area (MM/PB(GB)SA) methods. The results reveal that the heteroatom rich aromatic D-ring of liphagal extends towards the polar region of the binding site, and the D-ring 15-hydroxyl and 16-hydroxyl form three hydrogen bonds with Asp810 and Tyr836. The cyclohexyl A-ring projects up into the upper pocket of the lipophilic region, and the hydrophobic/van der Waals interactions with the residues Met772, Trp780, Ile800, Ile848, Val850, Met922, Phe930, Ile932 could be the key interactions for the affinity of liphagal to PI3Kα. Thus, a new strategy for the rational design of more potent analogs of liphagal against PI3Kα is provided. Our proposed PI3Kα/liphagal binding mode would be beneficial for the discovery of new active analogs of liphagal against PI3Kα.
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20
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An Algorithm to Identify Target-Selective Ligands - A Case Study of 5-HT7/5-HT1A Receptor Selectivity. PLoS One 2016; 11:e0156986. [PMID: 27271158 PMCID: PMC4896471 DOI: 10.1371/journal.pone.0156986] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
A computational procedure to search for selective ligands for structurally related protein targets was developed and verified for serotonergic 5-HT7/5-HT1A receptor ligands. Starting from a set of compounds with annotated activity at both targets (grouped into four classes according to their activity: selective toward each target, not-selective and not-selective but active) and with an additional set of decoys (prepared using DUD methodology), the SVM (Support Vector Machines) models were constructed using a selective subset as positive examples and four remaining classes as negative training examples. Based on these four component models, the consensus classifier was then constructed using a data fusion approach. The combination of two approaches of data representation (molecular fingerprints vs. structural interaction fingerprints), different training set sizes and selection of the best SVM component models for consensus model generation, were evaluated to determine the optimal settings for the developed algorithm. The results showed that consensus models with molecular fingerprints, a larger training set and the selection of component models based on MCC maximization provided the best predictive performance.
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21
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Sweidan K, Sabbah DA, Bardaweel S, Dush KA, Sheikha GA, Mubarak MS. Computer-aided design, synthesis, and biological evaluation of new indole-2-carboxamide derivatives as PI3Kα/EGFR inhibitors. Bioorg Med Chem Lett 2016; 26:2685-90. [PMID: 27084677 DOI: 10.1016/j.bmcl.2016.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/03/2016] [Accepted: 04/05/2016] [Indexed: 10/22/2022]
Abstract
Structure-based drug design and molecular modeling were employed to identify a new series of indole-2-carboxamides as potential anticancer agents. These compounds were synthesized and characterized with the aid of several spectroscopic techniques, such as FT-IR, NMR, and mass spectrometry as well as by elemental analysis. Molecular docking studies confirmed that the newly synthesized compounds accommodate PI3Kα and EGFR kinase catalytic sites and form H-bonding with the key binding residues. The antitumor activity of these new compounds against an array of cancer cell lines (human colon carcinoma (HCT116), leukemia (K562), and breast cancer (MDA231) was evaluated. Results revealed that these compounds were selective against the kinase domain, and none of them showed any inhibitory activity against K562. In addition, results showed that compound 13 exhibited high potency in HCT116 and MDA231 with IC50 values of 19 and 15μM, respectively. Our findings recommend that further optimization of this series would be beneficial for colon and breast cancer treatment.
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Affiliation(s)
- Kamal Sweidan
- Department of Chemistry, The University of Jordan, Amman 11942, Jordan.
| | - Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, PO Box 130, Amman 11733, Jordan.
| | - Sanaa Bardaweel
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Khadeja Abu Dush
- Department of Chemistry, The University of Jordan, Amman 11942, Jordan
| | - Ghassan Abu Sheikha
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, PO Box 130, Amman 11733, Jordan
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22
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Molecular modeling based approach, synthesis, and cytotoxic activity of novel benzoin derivatives targeting phosphoinostide 3-kinase (PI3Kα). Bioorg Med Chem Lett 2015; 25:3120-4. [DOI: 10.1016/j.bmcl.2015.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/24/2015] [Accepted: 06/02/2015] [Indexed: 01/22/2023]
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23
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Yuan H, Zhuang J, Hu S, Li H, Xu J, Hu Y, Xiong X, Chen Y, Lu T. Molecular modeling of exquisitely selective c-Met inhibitors through 3D-QSAR and molecular dynamics simulations. J Chem Inf Model 2014; 54:2544-54. [PMID: 25181449 DOI: 10.1021/ci500268s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
c-Met has been considered as an attractive target for developing antitumor agents. The highly selective c-Met inhibitors provide invaluable opportunities for the combination with other therapies safely to achieve the optimal efficacy. In this work, a series of triazolopyrazine c-Met inhibitors with exquisitely selectivity were investigated using a combination of molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular dynamics simulation. Comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models were developed to reveal the structural determinants for c-Met inhibition. Both models were validated to have high reliability and predictability, and contour map analysis suggested feature requirements for different substituents on the scaffold. It is worth noting that an important hydrogen bond rich region was identified in the unique narrow channel, which is distinct from other kinases. Molecular dynamics simulations and binding free energy calculations provided further support that suitable groups in this hydrogen bond rich region made great contributions to the binding of ligands. Moreover, hydrogen bonds with residues of the narrow channel were also indicated to be essential to improve the activity and selectivity. This study will facilitate the discovery and optimization of novel c-Met inhibitors with higher activity and selectivity.
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Affiliation(s)
- Haoliang Yuan
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine , Wuxi, 214063 Jiangsu, P. R. China
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24
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Taha MO, Al-Sha'er MA, Khanfar MA, Al-Nadaf AH. Discovery of nanomolar phosphoinositide 3-kinase gamma (PI3Kγ) inhibitors using ligand-based modeling and virtual screening followed by in vitro analysis. Eur J Med Chem 2014; 84:454-65. [PMID: 25050878 DOI: 10.1016/j.ejmech.2014.07.056] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/03/2014] [Accepted: 07/17/2014] [Indexed: 11/30/2022]
Abstract
Phosphoinositide 3-kinase gamma (PI3Kγ) is member of a family of enzymes involved in cancer pathogenesis. Accordingly, considerable efforts have been carried out to develop new PI3Kγ inhibitors. Towards this end we explored the pharmacophoric space of PI3Kγ using three diverse sets of inhibitors. Subsequently, we employed genetic algorithm-based QSAR analysis to select optimal combination of pharmacophoric models and physicochemical descriptors that can explain bioactivity variation within training inhibitors. Interestingly, two successful pharmacophores were selected within two statistically consistent QSAR models. The close similarity among the two binding models prompted us to merge them in a hybrid pharmacophore. The resulting model showed superior receiver operator characteristic curve (ROC) and closely resembled binding interactions seen in crystallographic ligand-PI3Kγ complexes. The resulting model was employed to screen the national cancer institute (NCI) list of compounds to search for new PI3Kγ ligands. After testing captured hits in vitro, 19 compounds showed nanomolar IC50 values against PI3Kγ. The chemical structures and purities of most potent hits were validated using NMR and MS experiments.
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Affiliation(s)
- Mutasem O Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman, Jordan.
| | | | - Mohammad A Khanfar
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
| | - Afaf H Al-Nadaf
- Department of Pharmaceutical Chemistry, Applied Science University, Amman, Jordan
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25
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Zhu J, Pan P, Li Y, Wang M, Li D, Cao B, Mao X, Hou T. Theoretical studies on beta and delta isoform-specific binding mechanisms of phosphoinositide 3-kinase inhibitors. MOLECULAR BIOSYSTEMS 2013; 10:454-66. [PMID: 24336903 DOI: 10.1039/c3mb70314b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) is known to be closely related to tumorigenesis and cell proliferation, and controls a variety of cellular processes, including proliferation, growth, apoptosis, migration, metabolism, etc. The PI3K family comprises eight catalytic isoforms, which are subdivided into three classes. Recently, the discovery of inhibitors that block a single isoform of PI3K has continued to attract special attention because they may have higher selectivity for certain tumors and less toxicity for healthy cells. The PI3Kβ and PI3Kδ share fewer studies than α/γ, and therefore, in this work, the combination of molecular dynamics simulations and free energy calculations was employed to explore the binding of three isoform-specific PI3K inhibitors (COM8, IC87114, and GDC-0941) to PI3Kβ or PI3Kδ. The isoform specificities of the studied inhibitors derived from the predicted binding free energies are in good agreement with the experimental data. In addition, the key residues critical for PI3Kβ or PI3Kδ selectivity were highlighted by decomposing the binding free energies into the contributions from individual residues. It was observed that although PI3Kβ and PI3Kδ share the conserved ATP-binding pockets, individual residues do behave differently, particularly the residues critical for PI3Kβ or PI3Kδ selectivity. It can be concluded that the inhibitor specificity between PI3Kβ and PI3Kδ is determined by the additive contributions from multiple residues, not just a single one. This study provides valuable information for understanding the isoform-specific binding mechanisms of PI3K inhibitors, and should be useful for the rational design of novel and selective PI3K inhibitors.
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Affiliation(s)
- Jingyu Zhu
- Cyrus Tang Hematology Center, Soochow University, Suzhou, Jiangsu 215123, China.
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26
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Bharadwaj VS, Dean AM, Maupin CM. Insights into the Glycyl Radical Enzyme Active Site of Benzylsuccinate Synthase: A Computational Study. J Am Chem Soc 2013; 135:12279-88. [DOI: 10.1021/ja404842r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vivek S. Bharadwaj
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - Anthony M. Dean
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
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27
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Li XY, He BF, Luo HJ, Huang NY, Deng WQ. 3-Acyl-5-hydroxybenzofuran derivatives as potential anti-estrogen breast cancer agents: A combined experimental and theoretical investigation. Bioorg Med Chem Lett 2013; 23:4617-21. [DOI: 10.1016/j.bmcl.2013.06.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/30/2013] [Accepted: 06/10/2013] [Indexed: 12/01/2022]
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