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Agarwal R, Pattarawat P, Duff MR, Wang HCR, Baudry J, Smith JC. Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors. Pharmaceuticals (Basel) 2024; 17:867. [PMID: 39065718 PMCID: PMC11279411 DOI: 10.3390/ph17070867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. However, engineering specificity is an important goal. Herein, we use molecular modeling approaches to identify and target potential novel pockets specific to Class IIA HDAC-HDAC4 at the interface between HDAC4 and the transcriptional corepressor component protein NCoR. These pockets were screened using an ensemble docking approach combined with consensus scoring to identify compounds with a different binding mechanism than the currently known HDAC modulators. Binding was compared in experimental assays between HDAC4 and HDAC3, which belong to a different family of HDACs. HDAC4 was significantly inhibited by compound 88402 but not HDAC3. Two other compounds (67436 and 134199) had IC50 values in the low micromolar range for both HDACs, which is comparable to the known inhibitor of HDAC4, SAHA (Vorinostat). However, both of these compounds were significantly weaker inhibitors of HDAC3 than SAHA and thus more selective, albeit to a limited extent. Five compounds exhibited activity on human breast carcinoma and/or urothelial carcinoma cell lines. The present result suggests potential mechanistic and chemical approaches for developing selective HDAC4 modulators.
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Affiliation(s)
- Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
| | - Pawat Pattarawat
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA; (P.P.); (H.-C.R.W.)
| | - Michael R. Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
| | - Hwa-Chain Robert Wang
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA; (P.P.); (H.-C.R.W.)
| | - Jerome Baudry
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA;
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
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2
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Kausar R, Zahoor AF, Tabassum H, Kamal S, Ahmad Bhat M. Synergistic Biomedical Potential and Molecular Docking Analyses of Coumarin-Triazole Hybrids as Tyrosinase Inhibitors: Design, Synthesis, In Vitro Profiling, and In Silico Studies. Pharmaceuticals (Basel) 2024; 17:532. [PMID: 38675492 PMCID: PMC11054269 DOI: 10.3390/ph17040532] [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: 03/24/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The tyrosinase enzyme has a vital role in the browning of vegetables and fruits and the biosynthesis of melanin. In this work, we synthesized a diverse library of coumarin-triazole hybrids, and these compounds were characterized by using suitable analytical techniques. Our research work extends beyond the synthetic effort to explore the therapeutic potential of these compounds. We put the synthesized compounds through meticulous in vitro screening against the tyrosinase enzyme, and these coumarin derivatives evinced good IC50 values in the range of 0.339 ± 0.25 µM to 14.06 ± 0.92 µM. In the library of synthesized compounds, six compounds were found to be more potent than standard ascorbic acid (IC50 = 11.5 ± 1.00), and among them, 17e and 17f, being the most active, exhibited remarkable anti-tyrosinase potential, with IC50 values of 0.339 ± 0.25 μM and 3.148 ± 0.23 μM, respectively. Furthermore, an in silico modeling study was carried out to determine the key interactions of these compounds with the tyrosinase protein (PDB ID: 2Y9X) and thus to authenticate our experimental findings. The quantitative SAR studies exhibited a good correlation between the synthesized derivatives of coumarin and their anti-tyrosinase activity. The docking studies verified the experimental results, and ligand 17e showed good interaction with the core residues of tyrosinase. This study not only expands the field of coumarin-triazole hybrid synthesis but also provides valuable insights for the development of novel tyrosinase inhibitors.
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Affiliation(s)
- Rukhsana Kausar
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Hina Tabassum
- Department of Pharmacology, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
| | - Shagufta Kamal
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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3
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Gu H, Yan W, Yang J, Liu B, Zhao X, Wang H, Xu W, Wang C, Chen Y, Dong Q, Zhu Q, Xu Y, Zou Y. Discovery of Highly Selective PARP7 Inhibitors with a Novel Scaffold for Cancer Immunotherapy. J Med Chem 2024; 67:1932-1948. [PMID: 38059836 DOI: 10.1021/acs.jmedchem.3c01764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
PARP7 plays a crucial role in cancer immunity. The inhibition of PARP7 has shown potential in boosting the immune response against cancer, making it an attractive target for cancer immunotherapy. Herein, we employed a rigid constraint strategy (reduction in molecular flexibility) to design and synthesize a series of novel indazole-7-carboxamide derivatives based on the structure of RBN-2397. Among these derivatives, (S)-XY-05 was identified as the most promising PARP7 inhibitor (IC50: 4.5 nM). Additionally, (S)-XY-05 showed enhanced selectivity toward PARP7 and improved pharmacokinetic properties (oral bioavailability: 94.60%) compared with RBN-2397 (oral bioavailability: 25.67%). In the CT26 syngeneic mouse model, monotherapy with (S)-XY-05 displayed a strong antitumor effect (TGI: 83%) by activating T-cell-mediated immunity within the tumor microenvironment. Collectively, we confirmed that (S)-XY-05 has profound effects on tumor immunity, which paves the way for future studies of PARP7 inhibitors that could be utilized in cancer immunotherapy.
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Affiliation(s)
- Hongfeng Gu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenxin Yan
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Jieping Yang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Beibei Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaolin Zhao
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Hongxia Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenbo Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Chenghao Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yang Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Qiuyi Dong
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Qihua Zhu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yungen Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Zou
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
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4
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Lombino J, Vallone R, Cimino M, Gulotta MR, De Simone G, Morando MA, Sabbatella R, Di Martino S, Fogazza M, Sarno F, Coronnello C, De Rosa M, Cipollina C, Altucci L, Perricone U, Alfano C. In-silico guided chemical exploration of KDM4A fragments hits. Clin Epigenetics 2023; 15:197. [PMID: 38129913 PMCID: PMC10740270 DOI: 10.1186/s13148-023-01613-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Lysine demethylase enzymes (KDMs) are an emerging class of therapeutic targets, that catalyse the removal of methyl marks from histone lysine residues regulating chromatin structure and gene expression. KDM4A isoform plays an important role in the epigenetic dysregulation in various cancers and is linked to aggressive disease and poor clinical outcomes. Despite several efforts, the KDM4 family lacks successful specific molecular inhibitors. RESULTS Herein, starting from a structure-based fragments virtual screening campaign we developed a synergic framework as a guide to rationally design efficient KDM4A inhibitors. Commercial libraries were used to create a fragments collection and perform a virtual screening campaign combining docking and pharmacophore approaches. The most promising compounds were tested in-vitro by a Homogeneous Time-Resolved Fluorescence-based assay developed for identifying selective substrate-competitive inhibitors by means of inhibition of H3K9me3 peptide demethylation. 2-(methylcarbamoyl)isonicotinic acid was identified as a preliminary active fragment, displaying inhibition of KDM4A enzymatic activity. Its chemical exploration was deeply investigated by computational and experimental approaches which allowed a rational fragment growing process. The in-silico studies guided the development of derivatives designed as expansion of the primary fragment hit and provided further knowledge on the structure-activity relationship. CONCLUSIONS Our study describes useful insights into key ligand-KDM4A protein interaction and provides structural features for the development of successful selective KDM4A inhibitors.
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Affiliation(s)
- Jessica Lombino
- Molecular Informatics Group, Fondazione Ri.MED, 90100, Palermo, Italy
- C4T S.r.l., Colosseum Combinatorial Chemistry Center, 00133, Rome, Italy
| | - Rosario Vallone
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Maura Cimino
- Target Identification and Screening Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | | | - Giada De Simone
- Molecular Informatics Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Maria Agnese Morando
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Raffaele Sabbatella
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy
| | | | - Mario Fogazza
- Target Identification and Screening Group, Fondazione Ri.MED, 90100, Palermo, Italy
- Axxam SpA, 20091, Bresso, MI, Italy
| | - Federica Sarno
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli", 80100, Naples, Italy
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713, Groningen, GZ, The Netherlands
| | | | - Maria De Rosa
- Medicinal Chemistry Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Chiara Cipollina
- Target Identification and Screening Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli", 80100, Naples, Italy
- BIOGEM, 83031, Ariano Irpino, AV, Italy
- IEOS-CNR, 80100, Naples, Italy
| | - Ugo Perricone
- Molecular Informatics Group, Fondazione Ri.MED, 90100, Palermo, Italy.
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy.
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5
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Zahoor AF, Hafeez F, Mansha A, Kamal S, Anjum MN, Raza Z, Khan SG, Javid J, Irfan A, Bhat MA. Bacterial Tyrosinase Inhibition, Hemolytic and Thrombolytic Screening, and In Silico Modeling of Rationally Designed Tosyl Piperazine-Engrafted Dithiocarbamate Derivatives. Biomedicines 2023; 11:2739. [PMID: 37893112 PMCID: PMC10603954 DOI: 10.3390/biomedicines11102739] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Piperazine is a privileged moiety that is a structural part of many clinical drugs. Piperazine-based scaffolds have attracted the attention of pharmaceutical and medicinal scientists to develop novel, efficient therapeutic agents owing to their significant and promising biological profile. In the current study, an ecofriendly ultrasonic-assisted synthetic approach was applied to achieve a novel series of 1-tosyl piperazine dithiocarbamate acetamide hybrids 4a-4j, which was evaluated for in vitro tyrosinase inhibition and thrombolytic and hemolytic cytotoxic activities. Among all the piperazine-based dithiocarbamate acetamide target molecules 4a-4j, the structural analogs 4d displayed excellent tyrosinase inhibition efficacy (IC50 = 6.88 ± 0.11 µM) which was better than the reference standard drugs kojic acid (30.34 ± 0.75 µM) and ascorbic acid (11.5 ± 1.00 µM), respectively, which was further confirmed by in silico induced-fit docking (IFD) simulation Good tyrosinase activities were exhibited by 4g (IC50 = 7.24 ± 0.15 µM), 4b (IC50 = 8.01 ± 0.11 µM) and 4c (IC50 = 8.1 ± 0.30 µM) dithiocarbamate acetamides, which were also better tyrosinase inhibitors than the reference drugs but were less active than the 4d structural hybrid. All the derivatives are less toxic, having values in the 0.29 ± 0.01% to 15.6 ± 0.5% range. The scaffold 4b demonstrated better hemolytic potential (0.29 ± 0.01%), while a remarkably high thrombolytic chemotherapeutic potential was displayed by analog 4e (67.3 ± 0.2%).
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Affiliation(s)
- Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.F.Z.); (F.H.); (S.G.K.); (A.I.)
| | - Freeha Hafeez
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.F.Z.); (F.H.); (S.G.K.); (A.I.)
- Department of Chemistry, Riphah International University Faisalabad, Faisalabad 38000, Pakistan
| | - Asim Mansha
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.F.Z.); (F.H.); (S.G.K.); (A.I.)
| | - Shagufta Kamal
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Muhammad Naveed Anjum
- Department of Applied Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Zohaib Raza
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, SA 5000, Australia;
| | - Samreen Gul Khan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.F.Z.); (F.H.); (S.G.K.); (A.I.)
| | - Jamila Javid
- Department of Chemistry, University of Sialkot, Sialkot 51310, Pakistan;
| | - Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.F.Z.); (F.H.); (S.G.K.); (A.I.)
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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Ragusa MA, Naselli F, Cruciata I, Volpes S, Schimmenti C, Serio G, Mauro M, Librizzi M, Luparello C, Chiarelli R, La Rosa C, Lauria A, Gentile C, Caradonna F. Indicaxanthin Induces Autophagy in Intestinal Epithelial Cancer Cells by Epigenetic Mechanisms Involving DNA Methylation. Nutrients 2023; 15:3495. [PMID: 37571432 PMCID: PMC10420994 DOI: 10.3390/nu15153495] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Autophagy is an evolutionarily conserved process critical in maintaining cellular homeostasis. Recently, the anticancer potential of autophagy inducers, including phytochemicals, was suggested. Indicaxanthin is a betalain pigment found in prickly pear fruit with antiproliferative and pro-apoptotic activities in colorectal cancer cells associated with epigenetic changes in selected methylation-silenced oncosuppressor genes. Here, we demonstrate that indicaxanthin induces the up-regulation of the autophagic markers LC3-II and Beclin1, and increases autophagolysosome production in Caco-2 cells. Methylomic studies showed that the indicaxanthin-induced pro-autophagic activity was associated with epigenetic changes. In addition to acting as a hypermethylating agent at the genomic level, indicaxanthin also induced significant differential methylation in 39 out of 47 autophagy-related genes, particularly those involved in the late stages of autophagy. Furthermore, in silico molecular modelling studies suggested a direct interaction of indicaxanthin with Bcl-2, which, in turn, influenced the function of Beclin1, a key autophagy regulator. External effectors, including food components, may modulate the epigenetic signature of cancer cells. This study demonstrates, for the first time, the pro-autophagic potential of indicaxanthin in human colorectal cancer cells associated with epigenetic changes and contributes to outlining its potential healthy effect in the pathophysiology of the gastrointestinal tract.
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Affiliation(s)
- Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Flores Naselli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Ilenia Cruciata
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Sara Volpes
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Chiara Schimmenti
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Graziella Serio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Maurizio Mauro
- Department of Obstetrics & Gynecology and Women’s Health, Michael F. Price Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Mariangela Librizzi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Claudio Luparello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
- NBFC—National Biodiversity Future Center, 90133 Palermo, Italy
| | - Roberto Chiarelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Chiara La Rosa
- Department of Life Sciences and Systems Biology, Neuroscience Institute Cavalieri Ottolenghi, University of Torino, 10124 Turin, Italy;
| | - Antonino Lauria
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Carla Gentile
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
| | - Fabio Caradonna
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (M.A.R.); (F.N.); (I.C.); (S.V.); (C.S.); (G.S.); (M.L.); (C.L.); (R.C.); (A.L.); (F.C.)
- NBFC—National Biodiversity Future Center, 90133 Palermo, Italy
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7
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Park J, Wasim S, Jung JH, Kim MH, Lee BC, Alam MM, Lee SY. Synthesis, In Silico and In Vitro Characterization of Novel N, N-Substituted Pyrazolopyrimidine Acetamide Derivatives for the 18KDa Translocator Protein (TSPO). Pharmaceuticals (Basel) 2023; 16:ph16040576. [PMID: 37111333 PMCID: PMC10142799 DOI: 10.3390/ph16040576] [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: 02/08/2023] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The translocator protein (TSPO) is an interesting biological target for molecular imaging and therapy because the overexpression of TSPO is associated with microglial activation caused by neuronal damage or neuroinflammation, and these activated microglia are involved in various central nervous system (CNS) diseases. The TSPO is a target for neuroprotective treatment, which is used with the aim of reducing microglial cell activation. The novel N,N-disubstituted pyrazolopyrimidine acetamides scaffold (GMA 7-17), which bears a fluorine atom and is directly linked to the phenyl moiety, was synthesized, and each of the novel ligands was characterized in vitro. All of the newly synthesized ligands displayed picomolar to nanomolar affinity for the TSPO. Particularly, an in vitro affinity study led to the discovery of 2-(5,7-diethyl-2-(4-fluorophenyl)pyrazolo [1,5-a]pyrimidin-3-yl)-N-ethyl-N-phenylacetamide GMA 15 (Ki = 60 pM), a novel TSPO ligand that exhibits a 61-fold enhancement in affinity compared to the reference standard DPA-714 (Ki = 3.66 nM). Molecular dynamic (MD) studies of the highest affinity binder, GMA 15, were carried out to check its time-dependent stability with the receptor compared to DPA-714 and PK11195. The hydrogen bond plot also indicated that GMA 15 formed higher hydrogen bonds compared to DPA-714 and PK11195. We anticipate that further optimization to enhance the potency in a cellular assay needs to be followed, but our strategy of identifying potential TSPO binding novel scaffolds may open up a new avenue to develop novel TSPO ligands suited for potential molecular imaging and a wide range of therapeutic applications.
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Affiliation(s)
- Jaekyung Park
- Gachon Advanced Institute for Health Science and Technology, Graduate School, Gachon University, Incheon 21999, Republic of Korea
| | - Sobia Wasim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Jae Ho Jung
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
| | - Mi-Hyun Kim
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Byung Chul Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea
- Center for Nanomolecular Imaging and Innovative Drug Development, Advanced Institutes of Convergence Technology, Suwon 16229, Republic of Korea
| | | | - Sang-Yoon Lee
- Gachon Advanced Institute for Health Science and Technology, Graduate School, Gachon University, Incheon 21999, Republic of Korea
- Neuroscience Research Institute, Gachon University, Incheon 20565, Republic of Korea
- Department of Neuroscience, College of Medicine, Gachon University, Incheon 21936, Republic of Korea
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8
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Patel S, Patel S, Tulsian K, Kumar P, Vyas VK, Ghate M. Design of 2-amino-6-methyl-pyrimidine benzoic acids as ATP competitive casein kinase-2 (CK2) inhibitors using structure- and fragment-based design, docking and molecular dynamic simulation studies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:211-230. [PMID: 37051759 DOI: 10.1080/1062936x.2023.2196091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Overexpression of casein kinase-2 (CK2) has been implicated in several carcinomas, mainly lung, prostate and acute myeloid leukaemia. The smaller nucleotide pocket compared to related kinases provides a great opportunity to discover newer ATP-competitive CK2 inhibitors. In this study, we have employed an integrated structure- and fragment-based design strategy to design 2-amino-6-methyl-pyrimidine benzoic acids as ATP-competitive CK2 inhibitors. A statistically significant four features-based E-pharmacophore (ARRR) model was used to screen 780,092 molecules. Further, the retrieved hits were considered for molecular docking study to identify essential binding interactions. At the same time, fragment-based virtual screening was performed using a dataset of 1,542,397 fragments. The identified hits and fragments were used as structure templates to rationalize the design of 2-amino-6-methyl-pyrimidine benzoic acids as newer CK2 inhibitors. Finally, the binding interactions of the designed hits were identified using an induced fit docking (IFD) study, and their stability was estimated by a molecular dynamics (MD) simulation study of 100 ns.
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Affiliation(s)
- S Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, India
| | - S Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad, India
| | - K Tulsian
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, India
| | - P Kumar
- Department of Botany, Bioinformatics and Climate Change Impacts Management, Gujarat University, Ahmedabad, India
| | - V K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, India
| | - M Ghate
- School of Pharmacy, National Forensic Science University, Gandhinagar, India
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9
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Design, synthesis and mechanistic studies of novel imidazo[1,2-a]pyridines as anticancer agents. Bioorg Chem 2022; 128:106042. [PMID: 35878430 DOI: 10.1016/j.bioorg.2022.106042] [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: 03/20/2022] [Revised: 05/16/2022] [Accepted: 07/17/2022] [Indexed: 11/20/2022]
Abstract
Herein, the design, synthesis and mechanistic study of five series of imidazo[1,2-a]pyridines 8a-d, 9a-f, 11a-c, 12a-d and 14a-d as anticancer agents were discussed. The cytotoxicity of imidazo[1,2-a]pyridine derivatives was screened against NCI 60 cancer cell lines. The cytotoxicity of compounds 8b, 8c, 9e and 9f was then evaluated against leukemia K-562 cancer cell line and normal lung fibroblasts (WI38). The hydrazone derivatives 8b and 8c exhibited significant cytotoxic activities against the leukemia K-562 cancer cell line with good safety margins (IC50 = 2.91 µM, SI = 8.32 and IC50 = 1.09 µM, SI = 10.54, respectively). In addition, compounds 8b, 8c, 9e and 9f were tested for their EGFR and COX-2 inhibitory activities. The hydrazone derivatives 8b and 8c were the most active EGFR inhibitors with IC50 values of 0.123 and 0.072 µM, respectively. Compound 8c selectively inhibited COX-2 (IC50 = 1.09 µM, SI = 13.78). Moreover, the potential of compound 8c to induce apoptosis in leukemia K-562 cell line was determined. Compound 8c showed a pre-G1 apoptosis and a growth arrest of leukemia K-562 cell line at G1 phase of cell cycle. Also, compound 8c was able to induce caspase-3 overexpression (6.98 folds), if compared to control. Finally, molecular docking studies and physicochemical properties calculation of compounds 8b, 8c, 9e and 9f were carried out to explain the biological data and to predict bioavailability of the most active compounds.
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10
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Babu S, Nagarajan SK, Sathish S, Negi VS, Sohn H, Madhavan T. Identification of Potent and Selective JAK1 Lead Compounds Through Ligand-Based Drug Design Approaches. Front Pharmacol 2022; 13:837369. [PMID: 35529449 PMCID: PMC9068899 DOI: 10.3389/fphar.2022.837369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/07/2022] [Indexed: 01/06/2023] Open
Abstract
JAK1 plays a significant role in the intracellular signaling by interacting with cytokine receptors in different types of cells and is linked to the pathogenesis of various cancers and in the pathology of the immune system. In this study, ligand-based pharmacophore modeling combined with virtual screening and molecular docking methods was incorporated to identify the potent and selective lead compounds for JAK1. Initially, the ligand-based pharmacophore models were generated using a set of 52 JAK1 inhibitors named C-2 methyl/hydroxyethyl imidazopyrrolopyridines derivatives. Twenty-seven pharmacophore models with five and six pharmacophore features were generated and validated using potency and selectivity validation methods. During potency validation, the Guner-Henry score was calculated to check the accuracy of the generated models, whereas in selectivity validation, the pharmacophore models that are capable of identifying selective JAK1 inhibitors were evaluated. Based on the validation results, the best pharmacophore models ADHRRR, DDHRRR, DDRRR, DPRRR, DHRRR, ADRRR, DDHRR, and ADPRR were selected and taken for virtual screening against the Maybridge, Asinex, Chemdiv, Enamine, Lifechemicals, and Zinc database to identify the new molecules with novel scaffold that can bind to JAK1. A total of 4,265 hits were identified from screening and checked for acceptable drug-like properties. A total of 2,856 hits were selected after ADME predictions and taken for Glide molecular docking to assess the accurate binding modes of the lead candidates. Ninety molecules were shortlisted based on binding energy and H-bond interactions with the important residues of JAK1. The docking results were authenticated by calculating binding free energy for protein–ligand complexes using the MM-GBSA calculation and induced fit docking methods. Subsequently, the cross-docking approach was carried out to recognize the selective JAK1 lead compounds. Finally, top five lead compounds that were potent and selective against JAK1 were selected and validated using molecular dynamics simulation. Besides, the density functional theory study was also carried out for the selected leads. Through various computational studies, we observed good potency and selectivity of these lead compounds when compared with the drug ruxolitinib. Compounds such as T5923555 and T5923531 were found to be the best and can be further validated using in vitro and in vivo methods.
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Affiliation(s)
- Sathya Babu
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, India
| | - Santhosh Kumar Nagarajan
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, India
| | - Sruthy Sathish
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, India
| | - Vir Singh Negi
- Department of Clinical Immunology, Jawaharlal Institute of Post-Graduate Medical Education and Research, Pondicherry, India
| | - Honglae Sohn
- Department of Chemistry and Department of Carbon Materials, Chosun University, Gwangju, South Korea
- *Correspondence: Thirumurthy Madhavan, ; Honglae Sohn,
| | - Thirumurthy Madhavan
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, India
- *Correspondence: Thirumurthy Madhavan, ; Honglae Sohn,
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11
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Novel sulfonyl thiazolyl-hydrazone derivatives as EGFR inhibitors: Design, synthesis, biological evaluation and molecular docking studies. Bioorg Chem 2022; 121:105684. [DOI: 10.1016/j.bioorg.2022.105684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/28/2021] [Accepted: 02/10/2022] [Indexed: 12/18/2022]
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12
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Halder D, Das S, Joseph A, Jeyaprakash RS. Molecular docking and dynamics approach to in silico drug repurposing for inflammatory bowels disease by targeting TNF alpha. J Biomol Struct Dyn 2022; 41:3462-3475. [PMID: 35285757 DOI: 10.1080/07391102.2022.2050948] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease is a chronic disorder of the large intestine with the prevalence of approximately 400 cases in 100000, and it is rising day by day. However, several drugs like sulfasalazine (composed of sulfapyridine and 5-aminosalicylic acid or 5-ASA), corticosteroids, and immunosuppressants manage the disease. But there are no absolute treatments for the pain and inflammation of the disease. TNFα is an important target, and drugs like infliximab and adalimumab have pharmacological potency but with pronounced toxicity. So, we choose this major target TNFα for the virtual screening of US-FDA-approved drugs for its repurposing using the in silico method. The protein TNFα (PDB ID: 2AZ5) with small molecule inhibitor and the US-FDA-approved drug molecules (from Zinc database) were first imported and prepared using Protein Preparation Wizard and LigPrep, respectively, followed by molecular docking, ADMET analysis and prime MMGBSA. After that, the drugs were shortlisted according to dock score, ADMET parameters and MM GBSA dG binding score. After that, the shortlisted drug molecules were subjected to an induced-fit docking analysis. Two of the most promising molecules, ZINC000003830957 (Iopromide) and ZINC000003830635 (Deferoxamine), were chosen for molecular dynamics simulation. Finally, the bioisosteric replacement was used to improve the ADMET properties of these molecules. This research provides an idea for drug exploration and computational tools for drug discovery in treating inflammatory bowel disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debojyoti Halder
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - R S Jeyaprakash
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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13
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Ahmad Mir S, Meher RK, Baitharu I, Nayak B. Molecular dynamic simulation, free binding energy calculation of Thiazolo-[2,3-b]quinazolinone derivatives against EGFR-TKD and their anticancer activity. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100418] [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] Open
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14
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Topomer-CoMFA proposed as a tool to construct dual EGFR/HER-2 models. J Mol Model 2021; 27:239. [PMID: 34363097 DOI: 10.1007/s00894-021-04852-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Protein kinases (in this case, HER-2 and EGFR) are involved in cancer-related diseases. Some reports have shown unique CoMFA models using the sum of activities expressed as pIC50 (-log IC50), as the classical CoMFA technique would not be the best strategy to construct models for multitarget therapy considering that the molecular alignment will not be the same for different targets. An alternative for this problem is the use of Topomer-CoMFA, a variation of CoMFA, which does not require the alignment step in the generation of 3D models. In this study, we propose the combined use of the sum of activities and Topomer-CoMFA for the construction of a unique dual 3D model considering the inhibitory activities against EGFR and HER-2. For this, 88 compounds from the literature were divided into two groups: training (71) and test (17) sets. The biological activity of each compound, expressed as IC50 for EGFR and HER-2, was transformed into pIC50, summed, and used as the dependent variable in the Topomer-CoMFA analyses. The obtained model was considered statistically robust in the prediction of the dual activity of new compounds. Finally, based on the obtained model, we proposed structural modifications to some of the compounds used to improve the biological data. From the 3D model, we suggested new derivative compounds with improved biological activity for both targets. Therefore, the combination of the techniques proposed in this study proves to be a good strategy to construct better statistical models that can predict biological activities in multitarget systems.
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15
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Lauria A, La Monica G, Terenzi A, Mannino G, Bonsignore R, Bono A, Almerico AM, Barone G, Gentile C, Martorana A. Antiproliferative Properties and G-Quadruplex-Binding of Symmetrical Naphtho[1,2-b:8,7-b']dithiophene Derivatives. Molecules 2021; 26:molecules26144309. [PMID: 34299583 PMCID: PMC8303715 DOI: 10.3390/molecules26144309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 12/04/2022] Open
Abstract
Background: G-quadruplex (G4) forming sequences are recurrent in telomeres and promoter regions of several protooncogenes. In normal cells, the transient arrangements of DNA in G-tetrads may regulate replication, transcription, and translation processes. Tumors are characterized by uncontrolled cell growth and tissue invasiveness and some of them are possibly mediated by gene expression involving G-quadruplexes. The stabilization of G-quadruplex sequences with small molecules is considered a promising strategy in anticancer targeted therapy. Methods: Molecular virtual screening allowed us identifying novel symmetric bifunctionalized naphtho[1,2-b:8,7-b’]dithiophene ligands as interesting candidates targeting h-Telo and c-MYC G-quadruplexes. A set of unexplored naphtho-dithiophene derivatives has been synthesized and biologically tested through in vitro antiproliferative assays and spectroscopic experiments in solution. Results: The analysis of biological and spectroscopic data highlighted noteworthy cytotoxic effects on HeLa cancer cell line (GI50 in the low μM range), but weak interactions with G-quadruplex c-MYC promoter. Conclusions: The new series of naphtho[1,2-b:8,7-b’]dithiophene derivatives, bearing the pharmacophoric assumptions necessary to stabilize G-quadruplexes, have been designed and successfully synthesized. The interesting antiproliferative results supported by computer aided rational approaches suggest that these studies are a significant starting point for a lead optimization process and the isolation of a more efficacious set of G-quadruplexes stabilizers.
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Affiliation(s)
- Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Gabriele La Monica
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Alessio Terenzi
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Via Quarello 15/A, 10135 Turin, Italy;
| | - Riccardo Bonsignore
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany;
| | - Alessia Bono
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Carla Gentile
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche “STEBICEF”, University of Palermo, Viale delle Scienze—Ed. 17, 90128 Palermo, Italy; (A.L.); (G.L.M.); (A.T.); (A.B.); (A.M.A.); (G.B.); (C.G.)
- Correspondence: ; Tel.: +39-091-2389-6821
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16
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Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors. Int J Mol Sci 2021; 22:ijms22116070. [PMID: 34199858 PMCID: PMC8200130 DOI: 10.3390/ijms22116070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
The approval of the first HIV-1 protease inhibitors (HIV-1 PRIs) marked a fundamental step in the control of AIDS, and this class of agents still represents the mainstay therapy for this illness. Despite the undisputed benefits, the necessary lifelong treatment led to numerous severe side-effects (metabolic syndrome, hepatotoxicity, diabetes, etc.). The HIV-1 PRIs are capable of interacting with "secondary" targets (off-targets) characterized by different biological activities from that of HIV-1 protease. In this scenario, the in-silico techniques undoubtedly contributed to the design of new small molecules with well-fitting selectivity against the main target, analyzing possible undesirable interactions that are already in the early stages of the research process. The present work is focused on a new mixed-hierarchical, ligand-structure-based protocol, which is centered on an on/off-target approach, to identify the new selective inhibitors of HIV-1 PR. The use of the well-established, ligand-based tools available in the DRUDIT web platform, in combination with a conventional, structure-based molecular docking process, permitted to fast screen a large database of active molecules and to select a set of structure with optimal on/off-target profiles. Therefore, the method exposed herein, could represent a reliable help in the research of new selective targeted small molecules, permitting to design new agents without undesirable interactions.
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17
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The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors. Sci Rep 2021; 11:9283. [PMID: 33927258 PMCID: PMC8085067 DOI: 10.1038/s41598-021-88630-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
The maturation of coronavirus SARS-CoV-2, which is the etiological agent at the origin of the COVID-19 pandemic, requires a main protease Mpro to cleave the virus-encoded polyproteins. Despite a wealth of experimental information already available, there is wide disagreement about the Mpro monomer-dimer equilibrium dissociation constant. Since the functional unit of Mpro is a homodimer, the detailed knowledge of the thermodynamics of this equilibrium is a key piece of information for possible therapeutic intervention, with small molecules interfering with dimerization being potential broad-spectrum antiviral drug leads. In the present study, we exploit Small Angle X-ray Scattering (SAXS) to investigate the structural features of SARS-CoV-2 Mpro in solution as a function of protein concentration and temperature. A detailed thermodynamic picture of the monomer-dimer equilibrium is derived, together with the temperature-dependent value of the dissociation constant. SAXS is also used to study how the Mpro dissociation process is affected by small inhibitors selected by virtual screening. We find that these inhibitors affect dimerization and enzymatic activity to a different extent and sometimes in an opposite way, likely due to the different molecular mechanisms underlying the two processes. The Mpro residues that emerge as key to optimize both dissociation and enzymatic activity inhibition are discussed.
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18
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Ullah MA, Johora FT, Sarkar B, Araf Y, Ahmed N, Nahar AN, Akter T. Computer-assisted evaluation of plant-derived β-secretase inhibitors in Alzheimer’s disease. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00150-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
Alzheimer’s disease (AD) is a progressive neurodegenerative age-related dementia that results in memory loss of elderly people. Many hypotheses have been formally articulated till now to decipher the pathogenesis of this disease. According to the compelling amyloidogenic hypothesis, β-secretase is a key regulatory enzyme in AD development and is therefore considered as one of the major targets for the development of drugs to treat AD. In this study, 40 plant-derived phytocompounds, proven to have β-secretase inhibitory activity in different laboratory experiments, were evaluated using computational approaches in order to identify the best possible β-secretase inhibitor(s).
Results
Amentoflavone (IFD score: − 7.842 Kcal/mol), Bilobetin (IFD score: − 7.417 Kcal/mol), and Ellagic acid (IFD score: − 6.923 Kcal/mol) showed highest β-secretase inhibitory activities with high binding affinity among all the selected phytocompounds and interacted with key amino acids, i.e., Asp32, Tyr71, and Asp228 in the catalytic site of β-secretase. Moreover, these three molecules exhibited promising results in different drug potential assessment experiments and displayed signs of correlation with significant pharmacological and biological activities.
Conclusion
Amentoflavone, Biolbetin, and Ellagic acid could be investigated further in developing β-secretase-dependent drug for the effective treatment of AD. However, additional in vivo and in vitro experiments might be required to strengthen the findings of this experiment.
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In Silico Identification of Small Molecules as New Cdc25 Inhibitors through the Correlation between Chemosensitivity and Protein Expression Pattern. Int J Mol Sci 2021; 22:ijms22073714. [PMID: 33918281 PMCID: PMC8038176 DOI: 10.3390/ijms22073714] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 01/11/2023] Open
Abstract
The cell division cycle 25 (Cdc25) protein family plays a crucial role in controlling cell proliferation, making it an excellent target for cancer therapy. In this work, a set of small molecules were identified as Cdc25 modulators by applying a mixed ligand-structure-based approach and taking advantage of the correlation between the chemosensitivity of selected structures and the protein expression pattern of the proposed target. In the first step of the in silico protocol, a set of molecules acting as Cdc25 inhibitors were identified through a new ligand-based protocol and the evaluation of a large database of molecular structures. Subsequently, induced-fit docking (IFD) studies allowed us to further reduce the number of compounds biologically screened. In vitro antiproliferative and enzymatic inhibition assays on the selected compounds led to the identification of new structurally heterogeneous inhibitors of Cdc25 proteins. Among them, J3955, the most active inhibitor, showed concentration-dependent antiproliferative activity against HepG2 cells, with GI50 in the low micromolar range. When J3955 was tested in cell-cycle perturbation experiments, it caused mitotic failure by G2/M-phase cell-cycle arrest. Finally, Western blotting analysis showed an increment of phosphorylated Cdk1 levels in cells exposed to J3955, indicating its specific influence in cellular pathways involving Cdc25 proteins.
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20
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Bansal Y, Minhas R, Singhal A, Arora RK, Bansal G. Benzimidazole: A Multifacted Nucelus for Anticancer Agents. CURR ORG CHEM 2021. [DOI: 10.2174/1385272825666210208141107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cancer is characterized by an uncontrolled proliferation of cells, dedifferentiation,
invasiveness and metastasis. Endothelial growth factor (eGF), insulin-like growth factor
(IGF), platelet-derived growth factor (PDGF), Fibroblast growth factor (FGF), Vascular endothelial
growth factor (VEGF), checkpoint kinase 1 & 2 ( Chk1 & Chk2), aurora kinases,
topoisomerases, histone deacetylators (HDAC), poly(ADP-Ribose)polymerase (PARP), farnesyl
transferases, RAS-MAPK pathway and PI3K-Akt-mTOR pathway, are some of the
prominent mediators implicated in the proliferation of tumor cells. Huge artillery of natural
and synthetic compounds as anticancer, which act by inhibiting one or more of the enzymes
and/or pathways responsible for the progression of tumor cells, is reported in the literature.
The major limitations of anticancer agents used in clinics as well as of those under development
in literature are normal cell toxicity and other side effects due to lack of specificity.
Hence, medicinal chemists across the globe have been working for decades to develop potent and safe anticancer
agents from natural sources as well as from different classes of heterocycles. Benzimidazole is one of the most important
and explored heteronucelus because of their versatility in biological actions as well as synthetic applications
in medicinal chemistry. The structural similarity of amino derivatives of benzimidazole with purines makes it a fascinating
nucleus for the development of anticancer, antimicrobial and anti-HIV agents. This review article is an attempt
to critically analyze various reports on benzimidazole derivatives acting on different targets to act as anticancer so as
to understand the structural requirements around benzimidazole nucleus for each target and enable medicinal chemists
to promote rational development of antitumor agents.
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Affiliation(s)
- Yogita Bansal
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala - 147002, India
| | - Richa Minhas
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala - 147002, India
| | - Ankit Singhal
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala - 147002, India
| | - Radhey Krishan Arora
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala - 147002, India
| | - Gulshan Bansal
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala - 147002, India
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21
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Mannino G, Iovino P, Lauria A, Genova T, Asteggiano A, Notarbartolo M, Porcu A, Serio G, Chinigò G, Occhipinti A, Capuzzo A, Medana C, Munaron L, Gentile C. Bioactive Triterpenes of Protium heptaphyllum Gum Resin Extract Display Cholesterol-Lowering Potential. Int J Mol Sci 2021; 22:ijms22052664. [PMID: 33800828 PMCID: PMC7961947 DOI: 10.3390/ijms22052664] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
Hypercholesterolemia is one of the major causes of cardiovascular disease, the risk of which is further increased if other forms of dyslipidemia occur. Current therapeutic strategies include changes in lifestyle coupled with drug administration. Statins represent the most common therapeutic approach, but they may be insufficient due to the onset of resistance mechanisms and side effects. Consequently, patients with mild hypercholesterolemia prefer the use of food supplements since these are perceived to be safer. Here, we investigate the phytochemical profile and cholesterol-lowering potential of Protium heptaphyllum gum resin extract (PHE). Chemical characterization via HPLC-APCI-HRMS2 and GC-FID/MS identified 13 compounds mainly belonging to ursane, oleanane, and tirucallane groups. Studies on human hepatocytes have revealed how PHE is able to reduce cholesterol production and regulate the expression of proteins involved in its metabolism. (HMGCR, PCSK9, LDLR, FXR, IDOL, and PPAR). Moreover, measuring the inhibitory activity of PHE against HMGR, moderate inhibition was recorded. Finally, molecular docking studies identified acidic tetra- and pentacyclic triterpenoids as the main compounds responsible for this action. In conclusion, our study demonstrates how PHE may be a useful alternative to contrast hypercholesterolemia, highlighting its potential as a sustainable multitarget natural extract for the nutraceutical industry that is rapidly gaining acceptance as a source of health-promoting compounds.
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Affiliation(s)
- Giuseppe Mannino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Piera Iovino
- Biosfered S.R.L., 10148 Turin, Italy; (P.I.); (A.A.)
| | - Antonino Lauria
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Tullio Genova
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (T.G.); (G.C.); (L.M.)
| | - Alberto Asteggiano
- Biosfered S.R.L., 10148 Turin, Italy; (P.I.); (A.A.)
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10125 Torino, Italy (C.M.)
| | - Monica Notarbartolo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Alessandra Porcu
- Abel Nutraceuticals S.R.L., 10148 Turin, Italy; (A.P.); (A.O.); (A.C.)
| | - Graziella Serio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
| | - Giorgia Chinigò
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (T.G.); (G.C.); (L.M.)
| | - Andrea Occhipinti
- Abel Nutraceuticals S.R.L., 10148 Turin, Italy; (A.P.); (A.O.); (A.C.)
| | - Andrea Capuzzo
- Abel Nutraceuticals S.R.L., 10148 Turin, Italy; (A.P.); (A.O.); (A.C.)
| | - Claudio Medana
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10125 Torino, Italy (C.M.)
| | - Luca Munaron
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (T.G.); (G.C.); (L.M.)
| | - Carla Gentile
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.M.); (A.L.); (M.N.); (G.S.)
- Correspondence: ; Tel.: +39-091-2388-6472
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Haribabu J, Alajrawy OI, Jeyalakshmi K, Balachandran C, Krishnan DA, Bhuvanesh N, Aoki S, Natarajan K, Karvembu R. N-substitution in isatin thiosemicarbazones decides nuclearity of Cu(II) complexes - Spectroscopic, molecular docking and cytotoxic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:118963. [PMID: 33017789 DOI: 10.1016/j.saa.2020.118963] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
The mono- (1) and bi-nuclear (2) copper(II) complexes containing N-substituted isatin thiosemicarbazone(s) were synthesized, and characterized by analytical and spectroscopic (UV-Visible, FT-IR and EPR) techniques. Bimetallic nature of complex 2 was confirmed by single crystal X-ray crystallography. The structures predicted by spectroscopic and crystallographic methods were validated by computational studies. From the spectroscopic, crystallographic and computational data, the structures were found to be distorted square planar for 1 and distorted square pyramidal for 2. Molecular docking studies showed hydrogen bonding and hydrophobic interactions of the complexes with tyrosinase kinase receptors. Complex 1 exhibited promising cytotoxic activity against Jurkat (leukemia) cell line, and complex 2 displayed more activity against HeLa S3 (cervical) and Jurkat cell lines with the IC50 values of 3.53 and 3.70 μM, respectively. Cytotoxicity of 1 (Jurkat) and 2 (Jurkat and HeLa S3) was better than that of cisplatin. Morphological changes in A549 (lung), HeLa S3 and Jurkat cell lines were examined in presence of the active complexes with the co-staining of Hoechst, AO (acridine orange) and EB (ethidium bromide) by fluorescence microscope.
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Affiliation(s)
- Jebiti Haribabu
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India; Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Othman I Alajrawy
- College of Applied Science, Department of Applied Chemistry, University of Fallujah, Fallujah 00964, Iraq
| | - Kumaramangalam Jeyalakshmi
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India; Department of Chemistry, M. Kumarasamy College of Engineering, Karur 639113, India
| | - Chandrasekar Balachandran
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Dhanabalan Anantha Krishnan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India
| | - Nattamai Bhuvanesh
- Department of Chemistry, Texas A & M University, College Station, TX 77842, USA
| | - Shin Aoki
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Karuppannan Natarajan
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science, Coimbatore 641 020, India
| | - Ramasamy Karvembu
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India.
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Lu Y, Yin W, Alam MS, Kadi AA, Jahng Y, Kwon Y, Rahman AFMM. Synthesis, Biological Evaluation and Molecular Docking Study of Cyclic Diarylheptanoids as Potential Anticancer Therapeutics. Anticancer Agents Med Chem 2021; 20:464-475. [PMID: 31763968 DOI: 10.2174/1871520619666191125130237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/07/2019] [Accepted: 10/16/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Cancer is one of the leading causes of mortality globally. To cope with cancer, it is necessary to develop anticancer drugs. Bioactive natural products, i.e. diarylheptanoids, have gained significant attention of researchers owing to their intriguing structures and potent biological activities. In this article, considering the development of anticancer drugs with enhanced selectivity towards cancerous cells, a series of Cyclic Diarylheptanoids (CDHs) are designed, synthesized and evaluated their biological activity. OBJECTIVE To establish an easy route for the synthesis of diarylheptanoids, and evaluate their antiproliferative, and topoisomerase-I & -IIα inhibitory activities, for developing potential anticancer drugs among CDHs. METHODS Diarylheptanoids were synthesized from reported linear diarylheptanoids using the classical Ullmann reaction. Antibacterial activity was evaluated by the filter paper disc diffusion method. Cell viability was assessed by measuring mitochondrial dehydrogenase activity with a Cell Counting Kit (CCK-8). Topoisomerases I and II (topo-I and -IIα) inhibitory activity was measured by the assessment of relaxation of supercoiled pBR322 plasmid DNA. IFD protocol of Schrodinger Maestro v11.1 was used to characterize the binding pattern of studied compounds with the ATPase domain of the human topo-IIα. RESULTS The synthesized CDHs were evaluated for their biological activities (antibacterial, antiproliferative, and topoisomerase-I & -IIα inhibitory activities, respectively). Leading to obtain a series of anticancer agents with the least inhibitory activities against different microbes, improving their selectivity for cancer cells. In brief, most of the synthesized CDHs had excellent antiproliferative activity against T47D (human breast cancer cell line). Pterocarine possessed the strongest activity (2i; IC50 = 0.63µM) against T47D. The cyclic diarylheptanoid 2b induced 30% inhibition of topoisomerase-IIα activity at 100μM compared with the reference of etoposide, which induced 72% inhibition. Among the tested compounds, galeon (2h) displayed very low activity against four bacterial strains. Compounds 2b, 2h, and 2i formed hydrogen bonds with Thr215, Asn91, Asn120, Ala167, Lys168 and Ile141 residues, which are important for binding of ligand compound to the ATPase binding site of topoisomerase IIα by acting as ATP competitive molecule validated by docking study. In silico Absorption, Distribution, Metabolism and Excretion (ADME) analysis revealed the predicted ADME parameters of the studied compounds which showed recommended values. CONCLUSION A series of CDHs were synthesized and evaluated for their antibacterial, antiproliferative, and topo-I & -IIα inhibitory activities. SARs study, molecular docking study and in silico ADME analysis were conducted. Five compounds exhibited excellent and selective antiproliferative activity against the human breast cancer cell line (T47D). Among them, a compound 2h showed topo-IIα activity by 30% at 100µM, which represented a moderate intensity of inhibition compared with etoposide. Three of them formed hydrogen bonds with Thr215, Asn91, Asn120, and Ala167 residues, which are considered as crucial residues for binding to the ATPase domain of topoisomerase IIα. According to in silico drug-likeness property analysis, three compounds are expected to show superiority over etoposide in case of absorption, distribution, metabolism and excretion.
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Affiliation(s)
- Yang Lu
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Korea
| | - Wencui Yin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad S Alam
- Department of Chemistry, Jagannath University, Dhaka 1100, Bangladesh
| | - Adnan A Kadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yurngdong Jahng
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Korea
| | - Youngjoo Kwon
- College of Pharmacy, Ewha Womans University, Seoul 03760, Korea
| | - A F M Motiur Rahman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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24
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Structure- and ligand- based studies to gain insight into the pharmacological implications of histamine H3 receptor. Struct Chem 2021. [DOI: 10.1007/s11224-020-01711-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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25
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Patel H, Ahmad I, Jadhav H, Pawara R, Lokwani D, Surana S. Investigating the Impact of Different Acrylamide (Electrophilic Warhead) on Osimertinib’s Pharmacological Spectrum by Molecular Mechanic and Quantum Mechanic Approach. Comb Chem High Throughput Screen 2020; 25:149-166. [DOI: 10.2174/1386207323666201204125524] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/14/2020] [Accepted: 10/24/2020] [Indexed: 11/22/2022]
Abstract
Background:
Lung cancer has become the prominent cause of the cancer-related deaths globally. More than 80
% of all lung cancers have been diagnosed with Non- Small Cell Lung Cancer (NSCLC). The USFDA approved osimertinib
to treat patients with metastatic T790M EGFR NSCLC on a regular basis in March 2017. Recently, C797S mutation to
osimertinib has been reported, which indicates the need for structural modification to overcome the problem of mutation.
Objective:
In this bioinformatics study, we have evaluated the impact of various acrylamide as an electrophilic warhead on
the activity and selectivity of osimertinib.
Result:
Osimertinib analouge 48, 50, 60, 61, 67, 75, 80, 86, 89, 92, 93, 116 and 124 were the most active and selective
compounds against T790M EGFR mutants compared to Osimertinib.
Conclusion:
These compounds also showed less inclination towards WT-EGFR.
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Affiliation(s)
- Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Harsha Jadhav
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Rahul Pawara
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Deepak Lokwani
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
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Lauria A, Mannino S, Gentile C, Mannino G, Martorana A, Peri D. DRUDIT: web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets. Bioinformatics 2020; 36:1562-1569. [PMID: 31605102 DOI: 10.1093/bioinformatics/btz783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/19/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION New in silico tools to predict biological affinities for input structures are presented. The tools are implemented in the DRUDIT (DRUgs DIscovery Tools) web service. The DRUDIT biological finder module is based on molecular descriptors that are calculated by the MOLDESTO (MOLecular DEScriptors TOol) software module developed by the same authors, which is able to calculate more than one thousand molecular descriptors. At this stage, DRUDIT includes 250 biological targets, but new external targets can be added. This feature extends the application scope of DRUDIT to several fields. Moreover, two more functions are implemented: the multi- and on/off-target tasks. These tools applied to input structures allow for predicting the polypharmacology and evaluating the collateral effects. RESULTS The applications described in the article show that DRUDIT is able to predict a single biological target, to identify similarities among biological targets, and to discriminate different target isoforms. The main advantages of DRUDIT for the scientific community lie in its ease of use by worldwide scientists and the possibility to be used also without specific, and often expensive, hardware and software. In fact, it is fully accessible through the WWW from any device to perform calculations. Just a click or a tap can start tasks to predict biological properties for new compounds or repurpose drugs, lead compounds, or unsuccessful compounds. To date, DRUDIT is supported by four servers each able to execute 8 jobs simultaneously. AVAILABILITY AND IMPLEMENTATION The web service is accessible at the www.drudit.com URL and its use is free of charge. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF"
| | - Salvatore Mannino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF"
| | - Carla Gentile
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF"
| | - Giuseppe Mannino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF"
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF"
| | - Daniele Peri
- Dipartimento di Ingegneria, University of Palermo, Palermo I-90128, Italy
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Zheng Z, Borbulevych OY, Liu H, Deng J, Martin RI, Westerhoff LM. MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment. J Chem Inf Model 2020; 60:5437-5456. [PMID: 32791826 PMCID: PMC7781189 DOI: 10.1021/acs.jcim.0c00618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
For decades, the
complicated energy surfaces found in macromolecular
protein:ligand structures, which require large amounts of computational
time and resources for energy state sampling, have been an inherent
obstacle to fast, routine free energy estimation in industrial drug
discovery efforts. Beginning in 2013, the Merz research group addressed
this cost with the introduction of a novel sampling methodology termed
“Movable Type” (MT). Using numerical integration methods,
the MT method reduces the computational expense for energy state sampling
by independently calculating each atomic partition function from an
initial molecular conformation in order to estimate the molecular
free energy using ensembles of the atomic partition functions. In
this work, we report a software package, the DivCon Discovery Suite
with the MovableType module from QuantumBio Inc., that performs this
MT free energy estimation protocol in a fast, fully encapsulated manner.
We discuss the computational procedures and improvements to the original
work, and we detail the corresponding settings for this software package.
Finally, we introduce two validation benchmarks to evaluate the overall
robustness of the method against a broad range of protein:ligand structural
cases. With these publicly available benchmarks, we show that the
method can use a variety of input types and parameters and exhibits
comparable predictability whether the method is presented with “expensive”
X-ray structures or “inexpensively docked” theoretical
models. We also explore some next steps for the method. The MovableType
software is available at http://www.quantumbioinc.com/
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Affiliation(s)
- Zheng Zheng
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Oleg Y Borbulevych
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Hao Liu
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Jianpeng Deng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Roger I Martin
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Lance M Westerhoff
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
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Moreno LM, Quiroga J, Abonia R, Lauria A, Martorana A, Insuasty H, Insuasty B. Synthesis, biological evaluation, and in silico studies of novel chalcone- and pyrazoline-based 1,3,5-triazines as potential anticancer agents. RSC Adv 2020; 10:34114-34129. [PMID: 35519030 PMCID: PMC9056798 DOI: 10.1039/d0ra06799g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/09/2020] [Indexed: 12/17/2022] Open
Abstract
A novel series of triazin-chalcones (7,8)a-g and triazin-N-(3,5-dichlorophenyl)pyrazolines (9,10)a-g were synthesized and evaluated for their anticancer activity against nine different cancer strains. Triazine ketones 5 and 6 were synthesized from the cyanuric chloride 1 by using stepwise nucleophilic substitution of the chlorine atom. These ketones were subsequently subjected to a Claisen-Schmidt condensation reaction with aromatic aldehydes affording chalcones (7,8)a-g. Then, N-(3,5-dichlorophenyl)pyrazolines (9,10)a-g were obtained by cyclocondensation reactions of the respective chalcones (7,8)a-g with 3,5-dichlorophenylhydrazine. Among all the evaluated compounds, chalcones 7d,g and 8g exhibited more potent in vitro anticancer activity, with outstanding GI50 values ranging from 0.422 to 14.9 μM and LC50 values ranging from 5.08 μM to >100 μM. In silico studies, for both ligand- and structure-based, were executed to explore the inhibitory nature of chalcones and triazine derivatives. The results suggested that the evaluated compounds could act as modulators of the human thymidylate synthase enzyme.
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Affiliation(s)
- Leydi M Moreno
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle A.A. 25360 Cali Colombia
| | - Jairo Quiroga
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle A.A. 25360 Cali Colombia
- Center for Bioinformatics and Photonics-CIBioFI A.A. 25360 Cali Colombia
| | - Rodrigo Abonia
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle A.A. 25360 Cali Colombia
- Center for Bioinformatics and Photonics-CIBioFI A.A. 25360 Cali Colombia
| | - Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF", Università di Palermo Viale delle Scienze Ed. 17 I-90128 Palermo Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF", Università di Palermo Viale delle Scienze Ed. 17 I-90128 Palermo Italy
| | - Henry Insuasty
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad de Nariño A.A. 1175 Pasto Colombia
| | - Braulio Insuasty
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle A.A. 25360 Cali Colombia
- Center for Bioinformatics and Photonics-CIBioFI A.A. 25360 Cali Colombia
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Ullah MA, Johora FT, Sarkar B, Araf Y, Rahman MH. Curcumin analogs as the inhibitors of TLR4 pathway in inflammation and their drug like potentialities: a computer-based study. J Recept Signal Transduct Res 2020; 40:324-338. [PMID: 32223496 DOI: 10.1080/10799893.2020.1742741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Toll-like receptor 4 (TLR4) pathway is one of the major pathways that mediate the inflammation in human body. There are different anti-inflammatory drugs available in the market which specifically act on different signaling proteins of TLR4 pathway but they do have few side effects and other limitations for intended use in human body. In this study, Curcumin and its different analogs have been analyzed as the inhibitors of signaling proteins, i.e. Cycloxygenase-2 (COX-2), inhibitor of kappaβ kinase (IKK) and TANK binding kinase-1 (TBK-1) of TLR4 pathway using different computational tools. Initially, three compounds were selected for respective target based on free binding energy among which different compounds were reported to have better binding affinity than commercially available drug (control). Upon continuous computational exploration with induced fit docking (IFD), 6-Gingerol, Yakuchinone A and Yakuchinone B were identified as the best inhibitors of COX-2, IKK, and TBK-1 respectively. Then their drug-like potentialities were analyzed in different experiments where they were also predicted to perform well. Hopefully, this study will uphold the efforts of researchers to identify anti-inflammatory drugs from natural sources.
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Affiliation(s)
- Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Fatema Tuz Johora
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, Faculty of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Hasanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
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Martorana A, Gentile C, Lauria A. In Silico Insights into the SARS CoV-2 Main Protease Suggest NADH Endogenous Defences in the Control of the Pandemic Coronavirus Infection. Viruses 2020; 12:v12080805. [PMID: 32722574 PMCID: PMC7472248 DOI: 10.3390/v12080805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022] Open
Abstract
COVID-19 is a pandemic health emergency faced by the entire world. The clinical treatment of the severe acute respiratory syndrome (SARS) CoV-2 is currently based on the experimental administration of HIV antiviral drugs, such as lopinavir, ritonavir, and remdesivir (a nucleotide analogue used for Ebola infection). This work proposes a repurposing process using a database containing approximately 8000 known drugs in synergy structure- and ligand-based studies by means of the molecular docking and descriptor-based protocol. The proposed in silico findings identified new potential SARS CoV-2 main protease (MPRO) inhibitors that fit in the catalytic binding site of SARS CoV-2 MPRO. Several selected structures are NAD-like derivatives, suggesting a relevant role of these molecules in the modulation of SARS CoV-2 infection in conditions of cell chronic oxidative stress. Increased catabolism of NAD(H) during protein ribosylation in the DNA damage repair process may explain the greater susceptibility of the elderly population to the acute respiratory symptoms of COVID-19. The molecular modelling studies proposed herein agree with this hypothesis.
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Martorana A, Lauria A. Design of antitumor drugs targeting c-kit receptor by a new mixed ligand-structure based method. J Mol Graph Model 2020; 100:107666. [PMID: 32659630 DOI: 10.1016/j.jmgm.2020.107666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 10/23/2022]
Abstract
An important challenge, in the medicinal chemistry field, is the research of novel forceful drugs to overcome tumor-acquired resistance. The c-Kit tyrosine kinase receptor (TKR) represents a suitable target for the carcinogenesis control of gastro-intestinal stromal (GIST), leukemia, and mastocytosis tumors; nevertheless, several hotspot mutations of the protein limit the efficacy of a few clinical administered TKRs inhibitors. In this study, a new in silico protocol based on ligand and structure-based combined method is proposed, with the aim to identify a set of new c-Kit inhibitors able to complex c-Kit mutated proteins. A recent and freely available web-server DRUDIT is used for the ligand-based method. The protocol application allows for identifying a new generation of potential TKR inhibitors, which, in silico, complex the V654A and T670I mutated proteins and potentially overcome resistant mutations (D816H). The structure-based analysis is performed by Induced Fit Docking (IFD) studies. The comparison between the explored ligands and well-known drugs highlights the possibility to overcome tumor-acquired resistance. The best-selected structures (630705 and SML1348) provide valuable binding affinities with the mutated c-Kit forms (respectively T670I and V654A).
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Affiliation(s)
- Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF" - University of Palermo, Viale delle Scienze - Ed. 17, 90128, Palermo, Italy
| | - Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche "STEBICEF" - University of Palermo, Viale delle Scienze - Ed. 17, 90128, Palermo, Italy.
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32
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Sohraby F, Aryapour H. Rational drug repurposing for cancer by inclusion of the unbiased molecular dynamics simulation in the structure-based virtual screening approach: Challenges and breakthroughs. Semin Cancer Biol 2020; 68:249-257. [PMID: 32360530 DOI: 10.1016/j.semcancer.2020.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 03/07/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Managing cancer is now one of the biggest concerns of health organizations. Many strategies have been developed in drug discovery pipelines to help rectify this problem and two of the best ones are drug repurposing and computational methods. The combination of these approaches can have immense impact on the course of drug discovery. In silico drug repurposing can significantly reduce the time, the cost and the effort of drug development. Computational methods such as structure-based drug design (SBDD) and virtual screening can predict the potentials of small molecule binders, such as drugs, for having favorable effect on a particular molecular target. However, the demand for accuracy and efficiency of SBDD requires more sophisticated and complicated approaches such as unbiased molecular dynamics (UMD) simulation that has been recently introduced. As a complementary strategy, the knowledge acquired from UMD simulations can increase the chance of finding the right candidates and the pipeline of its administration is introduced and discussed in this review. An elaboration of this pipeline is also made by detailing an example, the binding and unbinding pathways of dasatinib-c-Src kinase complex, which shows that how influential this method can be in rational drug repurposing in cancer treatment.
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Affiliation(s)
- Farzin Sohraby
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran.
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Patel HM, Shaikh M, Ahmad I, Lokwani D, Surana SJ. BREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non small cell lung cancer (NSCLC). J Biomol Struct Dyn 2020; 39:2838-2856. [PMID: 32276580 DOI: 10.1080/07391102.2020.1754918] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the all existing drugs. In this work, we have reported the novel T790M/C797S-EGFR Tyrosine Kinase inhibitors using BREED based de novo hybridization approach. BREED generates novel inhibitors from structures of known ligands bound to a common target. Among the generated hybridised breed compounds, the top best scorer breed molecules were breed 436, breed 530, breed 450, breed 562 and breed 313. Molecular Dynamics simulation of breed 436 for 10 ns further suggested that docked compound was stable into the pocket of the T790M/C797S-EGFR Tyrosine Kinase. In silico pharmacokinetic predictions of the breed hybridised compounds were within the defined range described for human use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harun M Patel
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Matin Shaikh
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Iqrar Ahmad
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Deepak Lokwani
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
| | - Sanjay J Surana
- Division of Bioinformatics, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India
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Patel HM, Ahmad I, Pawara R, Shaikh M, Surana S. In silico search of triple mutant T790M/C797S allosteric inhibitors to conquer acquired resistance problem in non-small cell lung cancer (NSCLC): a combined approach of structure-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:1491-1505. [PMID: 32102624 DOI: 10.1080/07391102.2020.1734092] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the all existing drugs. Recently, EAI045 fourth-generation allosteric EGFR inhibitor has been reported, which binds away from the ATP-binding site and not rely on Cys 797 binding. Here, we are reporting compound ZINC20531199 by virtual based screening studies as allosteric inhibitor to overcome the EGFR T790M/C797S Tyrosine Kinase (TK) mutation problem. Molecular Dynamics simulation for 10 ns further suggested that docked compound ZINC20531199 was stable into the allosteric pocket of the C797S EGFR tyrosine kinase. In silico pharmacokinetic predictions of the virtually screened compounds are within the defined range described for human use. Results indicate that the virtual screened compounds could be potential leads for the further development of new allosteric EGFR T790M/C797S inhibitors to overcome the problem of drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harun M Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Rahul Pawara
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Matin Shaikh
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
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Kikiowo B, Ogunleye AJ, Inyang OK, Adelakun NS, Omotuyi OI, Metibemu DS, David TI, Oludoyi OO, Ijatuyi TT. Flavones scaffold of Chromolaena odorata as a potential xanthine oxidase inhibitor: Induced Fit Docking and ADME studies. ACTA ACUST UNITED AC 2019; 10:227-234. [PMID: 32983938 PMCID: PMC7502905 DOI: 10.34172/bi.2020.29] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/02/2019] [Accepted: 10/13/2019] [Indexed: 12/12/2022]
Abstract
Introduction: Gout is a type of painful inflammation initiated by the interactions between monosodium urate crystals and connective tissue. Xanthine oxidase (XO) catalyzes the oxidation of hypoxanthine to xanthine, then to uric acid. The primary treatments for gout include XO inhibitors. At present, allopurinol is the most used XO inhibitor for the treatment of gout. However, it can cause adverse effects commonly known as allopurinol hypersensitivity syndrome, thereby limiting its usage. Consequently, it is necessary to develop potent and less toxic inhibitors of XO. Chromolaena odorata is one of such plants under investigation for its diverse health benefits. Methods: Phytochemicals of C. odorata were screened against XO receptor, using molecular docking. The top five hit compounds of glide docking yield flavones scaffold which were subjected to induced fit docking (IFD) and absorption, distribution, metabolism, and excretion (ADME) studies. Results: The result showed that flavones scaffold of C. odorata can bind with higher affinity and lower free energy values when compared to that of the standard, allopurinol. The IFD scores of the flavones scaffold range from -1525.25 to -1527.99 kcal/mol. Conclusion: Our results have shown that flavones scaffold might have the potential to act as an effective drug candidate when compared to allopurinol in treating and/or preventing gout and some inflammatory condition.
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Affiliation(s)
- Babatomiwa Kikiowo
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Adewale Joseph Ogunleye
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Olumide Kayode Inyang
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Niyi Samuel Adelakun
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Olaposi Idowu Omotuyi
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Damilohun Samuel Metibemu
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Temitope Israel David
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Oluwatoyin Olajide Oludoyi
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Taiwo Tolulope Ijatuyi
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
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Kwofie SK, Broni E, Teye J, Quansah E, Issah I, Wilson MD, Miller WA, Tiburu EK, Bonney JHK. Pharmacoinformatics-based identification of potential bioactive compounds against Ebola virus protein VP24. Comput Biol Med 2019; 113:103414. [PMID: 31536833 DOI: 10.1016/j.compbiomed.2019.103414] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The impact of Ebola virus disease (EVD) is devastating with concomitant high fatalities. Currently, various drugs and vaccines are at different stages of development, corroborating the need to identify new therapeutic molecules. The VP24 protein of the Ebola virus (EBOV) plays a key role in the pathology and replication of the EVD. The VP24 protein interferes with the host immune response to viral infections and promotes nucleocapsid formation, thus making it a viable drug target. This study sought to identify putative lead compounds from the African flora with potential to inhibit the activity of the EBOV VP24 protein using pharmacoinformatics and molecular docking. METHODS An integrated library of 7675 natural products originating from Africa obtained from the AfroDB and NANPDB databases, as well as known inhibitors were screened against VP24 (PDB ID: 4M0Q) utilising AutoDock Vina after energy minimization using GROMACS. The top 19 compounds were physicochemically and pharmacologically profiled using ADMET Predictor™, SwissADME and DataWarrior. The mechanisms of binding between the molecules and EBOV VP24 were characterised using LigPlot+. The performance of the molecular docking was evaluated by generating a receiver operating characteristic (ROC) by screening known inhibitors and decoys against EBOV VP24. The prediction of activity spectra for substances (PASS) and machine learning-based Open Bayesian models were used to predict the anti-viral and anti-Ebola activity of the molecules, respectively. RESULTS Four natural products, namely, ZINC000095486070, ZINC000003594643, ZINC000095486008 and sarcophine were found to be potential EBOV VP24-inhibitiory molecules. The molecular docking results showed that ZINC000095486070 had high binding affinity of -9.7 kcal/mol with EBOV VP24, which was greater than those of the known VP24-inhibitors used as standards in the study including Ouabain, Nilotinib, Clomiphene, Torimefene, Miglustat and BCX4430. The area under the curve of the generated ROC for evaluating the performance of the molecular docking was 0.77, which was considered acceptable. The predicted promising molecules were also validated using induced-fit docking with the receptor using Schrödinger and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The molecules had better binding mechanisms and were pharmacologically profiled to have plausible efficacies, negligible toxicity as well as suitable for designing anti-Ebola scaffolds. ZINC000095486008 and sarcophine (NANPDB135) were predicted to possess anti-viral activity, while ZINC000095486070 and ZINC000003594643 to be anti-Ebola compounds. CONCLUSION The identified compounds are potential inhibitors worthy of further development as EBOV biotherapeutic agents. The scaffolds of the compounds could also serve as building blocks for designing novel Ebola inhibitors.
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Affiliation(s)
- Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana; West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana; Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA.
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Joshua Teye
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Erasmus Quansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Ibrahim Issah
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Michael D Wilson
- Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA; Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Whelton A Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA; Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Elvis K Tiburu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana; West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Joseph H K Bonney
- Department of Virology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
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Patel H, Ansari A, Pawara R, Ansari I, Jadhav H, Surana S. Design and synthesis of novel 2,4-disubstituted aminopyrimidines: reversible non-covalent T790M EGFR inhibitors. J Recept Signal Transduct Res 2019; 38:393-412. [DOI: 10.1080/10799893.2018.1557207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Azim Ansari
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Rahul Pawara
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Iqrar Ansari
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Harsha Jadhav
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
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Sindhu T, Venkatesan T, Prabhu D, Jeyakanthan J, Gracy GR, Jalali SK, Rai A. Insecticide-resistance mechanism of Plutella xylostella (L.) associated with amino acid substitutions in acetylcholinesterase-1: A molecular docking and molecular dynamics investigation. Comput Biol Chem 2018; 77:240-250. [DOI: 10.1016/j.compbiolchem.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/01/2018] [Accepted: 09/03/2018] [Indexed: 01/22/2023]
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Kwofie SK, Dankwa B, Odame EA, Agamah FE, Doe LPA, Teye J, Agyapong O, Miller WA, Mosi L, Wilson MD. In Silico Screening of Isocitrate Lyase for Novel Anti-Buruli Ulcer Natural Products Originating from Africa. Molecules 2018; 23:E1550. [PMID: 29954088 PMCID: PMC6100440 DOI: 10.3390/molecules23071550] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/16/2018] [Accepted: 06/25/2018] [Indexed: 12/15/2022] Open
Abstract
Buruli ulcer (BU) is caused by Mycobacterium ulcerans and is predominant in both tropical and subtropical regions. The neglected debilitating disease is characterized by chronic necrotizing skin lesions attributed to a mycolactone, which is a macrolide toxin secreted by M. ulcerans. The preferred treatment is surgical excision of the lesions followed by a prolonged combination antibiotic therapy using existing drugs such as rifampicin and streptomycin or clarithromycin. These antibiotics appear not to be adequately potent and efficacious against persistent and late stage ulcers. In addition, emerging drug resistance to treatment poses great challenges. There is a need to identify novel natural product-derived lead compounds, which are potent and efficacious for the treatment of Buruli ulcer. Natural products present a rich diversity of chemical compounds with proven activity against various infectious diseases, and therefore, are considered in this study. This study sought to computationally predict natural product-derived lead compounds with the potential to be developed further into potent drugs with better therapeutic efficacy than the existing anti-buruli ulcer compounds. The three-dimensional (3D) structure of Isocitrate lyase (ICL) of Mycobacterium ulcerans was generated using homology modeling and was further scrutinized with molecular dynamics simulations. A library consisting of 885 compounds retrieved from the AfroDb database was virtually screened against the validated ICL model using AutoDock Vina. AfroDb is a compendium of “drug-like” and structurally diverse 3D structures of natural products originating from different geographical regions in Africa. The molecular docking with the ICL model was validated by computing a Receiver Operating Characteristic (ROC) curve with a reasonably good Area Under the Curve (AUC) value of 0.89375. Twenty hit compounds, which docked firmly within the active site pocket of the ICL receptor, were assessed via in silico bioactivity and pharmacological profiling. The three compounds, which emerged as potential novel leads, comprise ZINC38143792 (Euscaphic acid), ZINC95485880, and ZINC95486305 with reasonable binding energies (high affinity) of −8.6, −8.6, and −8.8 kcal/mol, respectively. Euscaphic acid has been reported to show minimal inhibition against a drug-sensitive strain of M. tuberculosis. The other two leads were both predicted to possess dermatological activity while one was antibacterial. The leads have shown promising results pertaining to efficacy, toxicity, pharmacokinetic, and safety. These leads can be experimentally characterized to assess their anti-mycobacterial activity and their scaffolds may serve as rich skeletons for developing anti-buruli ulcer drugs.
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Affiliation(s)
- Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
- Department of Biochemistry, Cell and Molecular Biology, West African Center for Cell Biology and Infectious Pathogens, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Bismark Dankwa
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Emmanuel A Odame
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Francis E Agamah
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Lady P A Doe
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Joshua Teye
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Odame Agyapong
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Whelton A Miller
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Department of Chemistry & Physics, College of Science and Technology, Lincoln University, Philadelphia, PA 19104, USA.
| | - Lydia Mosi
- Department of Biochemistry, Cell and Molecular Biology, West African Center for Cell Biology and Infectious Pathogens, University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P. O. Box LG 77, Legon, Accra, Ghana.
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Sakkiah S, Kusko R, Pan B, Guo W, Ge W, Tong W, Hong H. Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations. Front Pharmacol 2018; 9:492. [PMID: 29867496 PMCID: PMC5962723 DOI: 10.3389/fphar.2018.00492] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/25/2018] [Indexed: 01/28/2023] Open
Abstract
When a small molecule binds to the androgen receptor (AR), a conformational change can occur which impacts subsequent binding of co-regulator proteins and DNA. In order to accurately study this mechanism, the scientific community needs a crystal structure of the Wild type AR (WT-AR) ligand binding domain, bound with antagonist. To address this open need, we leveraged molecular docking and molecular dynamics (MD) simulations to construct a structure of the WT-AR ligand binding domain bound with antagonist bicalutamide. The structure of mutant AR (Mut-AR) bound with this same antagonist informed this study. After molecular docking analysis pinpointed the suitable binding orientation of a ligand in AR, the model was further optimized through 1 μs of MD simulations. Using this approach, three molecular systems were studied: (1) WT-AR bound with agonist R1881, (2) WT-AR bound with antagonist bicalutamide, and (3) Mut-AR bound with bicalutamide. Our structures were very similar to the experimentally determined structures of both WT-AR with R1881 and Mut-AR with bicalutamide, demonstrating the trustworthiness of this approach. In our model, when WT-AR is bound with bicalutamide, Val716/Lys720/Gln733, or Met734/Gln738/Glu897 move and thus disturb the positive and negative charge clumps of the AF2 site. This disruption of the AF2 site is key for understanding the impact of antagonist binding on subsequent co-regulator binding. In conclusion, the antagonist induced structural changes in WT-AR detailed in this study will enable further AR research and will facilitate AR targeting drug discovery.
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Affiliation(s)
- Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Rebecca Kusko
- Immuneering Corporation, Cambridge, MA, United States
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Wenjing Guo
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Weigong Ge
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
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Patel H, Pawara R, Surana S. In-silico evidences for binding of Glucokinase activators to EGFR C797S to overcome EGFR resistance obstacle with mutant-selective allosteric inhibition. Comput Biol Chem 2018; 74:167-189. [PMID: 29627693 DOI: 10.1016/j.compbiolchem.2018.03.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/19/2018] [Accepted: 03/25/2018] [Indexed: 12/21/2022]
Abstract
The tyrosine kinase inhibitors (TKI) against epidermal growth factor receptor (EGFR) are generally utilized as a part of patients with non-small cell lung carcinoma (NSCLC). However, EGFR T790M mutation results in resistance to most clinically available EGFR TKIs. Third-generation EGFR TKIs against the T790M mutation has been in active clinical development to triumph the resistance problem; they covalently bind with conserved Cys797 inside the EGFR active site, offering both potency and kinase-selectivity. Third generation drugs target C797, which makes the C797S resistance mutation more subtle. EGFR C797S mutation was accounted to be a main mechanism of resistance to the third-generation inhibitors. The C797S mutation gives off an impression of being an ideal target for conquering the acquired resistance to the third generation inhibitors. We have performed structure based-virtual screening strategies for binding of glucokinase activator to EGFR C797S, which can overcome EGFR resistance impediment with mutant-selective allosteric inhibition towards all kinds of mutant EGFR (T790M, L858R, TMLR) and WT EGFR. The final filter of Lipinski's Rule of Five, Jargan's Rule of Three and in silico ADME predictions gave 23 hits, which conform to Lipinski's rule and Jorgensen's rule and all their pharmacokinetic parameters are inside the appropriate range characterized for human use, in this manner demonstrating their potential as a drug-like molecule.
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Affiliation(s)
- Harun Patel
- Division of Computer Aided Drug Design, Dept. of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425 405, Maharashtra, India.
| | - Rahul Pawara
- Division of Computer Aided Drug Design, Dept. of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425 405, Maharashtra, India.
| | - Sanjay Surana
- Division of Computer Aided Drug Design, Dept. of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425 405, Maharashtra, India
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In search of selective 11β-HSD type 1 inhibitors without nephrotoxicity: An approach to resolve the metabolic syndrome by virtual based screening. ARAB J CHEM 2018. [DOI: 10.1016/j.arabjc.2015.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Synthesis, molecular docking and biological evaluation of some benzimidazole derivatives as potent pancreatic lipase inhibitors. Bioorg Chem 2018; 76:478-486. [DOI: 10.1016/j.bioorg.2017.12.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 02/02/2023]
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Venkatesan A, Rambabu M, Jayanthi S, Febin Prabhu Dass J. Pharmacophore feature prediction and molecular docking approach to identify novel anti-HCV protease inhibitors. J Cell Biochem 2017; 119:960-966. [PMID: 28691304 DOI: 10.1002/jcb.26262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/05/2017] [Indexed: 02/06/2023]
Abstract
Discovering a potential drug for HCV treatment is a challenging task in the field of drug research. This study initiates with computational screening and modeling of promising ligand molecules. The foremost modeling method involves the identification of novel compound and its molecular interaction based on pharmacophore features. A total of 197 HCV compounds for NS3/4A protein target were screened for our study. The pharmacophore models were generated using PHASE module implemented in Schrodinger suite. The pharmacophore features include one hydrogen bond acceptor, one hydrogen bond donor, and three hydrophobic sites. As a result, based on mentioned hypothesis the model ADHHH.159 corresponds to the CID 59533233. Furthermore, docking was performed using maestro for all the 197 compounds. Among these, the CID 59533313 and 59533233 possess the best binding energy of -11.75 and -10.40 kcal/mol, respectively. The interactions studies indicated that the CID complexed with the NS3/4A protein possess better binding affinity with the other compounds. Further the compounds were subjected to calculate the ADME properties. Therefore, it can be concluded that these two compounds could be a potential alternative drug for the development of HCV.
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Affiliation(s)
- Arthi Venkatesan
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - Majji Rambabu
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - Sivaraman Jayanthi
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - J Febin Prabhu Dass
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
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Yang C, Di P, Fu J, Xiong H, Jing Q, Ren G, Tang Y, Zheng W, Liu G, Ren F. Improving the physicochemical properties of bicalutamide by complex formation with bovine serum albumin. Eur J Pharm Sci 2017; 106:381-392. [DOI: 10.1016/j.ejps.2017.05.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 11/27/2022]
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Ugale VG, Patel HM, Surana SJ. Molecular modeling studies of quinoline derivatives as VEGFR-2 tyrosine kinase inhibitors using pharmacophore based 3D QSAR and docking approach. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2013.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Zhu X, Zhou L, Zhong L, Dai D, Hong M, You R, Wang T. Exploration of potential RSK2 inhibitors by pharmacophore modelling, structure-based 3D-QSAR, molecular docking study and molecular dynamics simulation. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1274987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Xiaohong Zhu
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
| | - Lu Zhou
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
| | - Liangliang Zhong
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
| | - Duoqian Dai
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
| | - Meiyuan Hong
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
| | - Rong You
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
| | - Taijin Wang
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
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Das A, Bhattacharya S. Different Types of Molecular Docking Based on Variations of Interacting Molecules. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Molecular docking plays an important role in drug discovery research by facilitating target identification, target validation, virtual screening for lead identification and lead optimization. Depending upon the nature of the disease of interest, targets can be either protein or DNA while drugs are mostly organic small molecules. Different types of molecular docking techniques like protein-protein or protein-DNA or protein-small molecule or DNA-small molecule are employed for achieving the above mentioned objectives. This chapter provides a clear idea of the position of molecular docking in drug discovery with detailed discussion on different types of molecular docking based on the varieties of interacting partners. Subsequently the authors provide a detailed list of tools that can be used for docking in drug discovery and discus some examples of molecular docking in drug discovery before concluding with a remark on future areas of improvement in molecular docking related to drug discovery.
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Synthesis, Antimicrobial and In Silico EGFR Inhibitory Activity Evaluation of Sulfonylamino Pyrrolidine Derivatives. Pharm Chem J 2016. [DOI: 10.1007/s11094-016-1467-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Ugale VG, Bari SB. Structural Exploration of Quinazolin-4(3H)-ones as Anticonvulsants: Rational Design, Synthesis, Pharmacological Evaluation, and Molecular Docking Studies. Arch Pharm (Weinheim) 2016; 349:864-880. [DOI: 10.1002/ardp.201600218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Vinod G. Ugale
- Department of Pharmaceutical Chemistry; R. C. Patel Institute of Pharmaceutical Education and Research; Shirpur (Dhule) Maharashtra India
| | - Sanjay B. Bari
- Department of Pharmaceutical Chemistry; H. R. Patel Institute of Pharmaceutical Education and Research; Shirpur (Dhule) Maharashtra India
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