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Ahmad S, Bano N, Khanna K, Gupta D, Raza K. Reporting multitargeted potency of Tiaprofenic acid against lung cancer: Molecular fingerprinting, MD simulation, and MTT-based cell viability assay studies. Int J Biol Macromol 2024; 276:133872. [PMID: 39019378 DOI: 10.1016/j.ijbiomac.2024.133872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
Lung Cancer (LC) is among the most death-causing cancers, has caused the most destruction and is a gender-neutral cancer, and WHO has kept this cancer on its priority list to find the cure. We have used high-throughput virtual screening, standard precision docking, and extra precise docking for extensive screening of Drug Bank compounds, and the uniqueness of this study is that it considers multiple protein targets of prognosis and metastasis of LC. The docking and MM\GBSA calculation scores for the Tiaprofenic acid (DB01600) against all ten proteins range from -8.422 to -5.727 kcal/mol and - 47.43 to -25.72 kcal/mol, respectively. Also, molecular fingerprinting helped us to understand the interaction pattern of Tiaprofenic acid among all the proteins. Further, we extended our analysis to the molecular dynamic simulation in a neutralised SPC water medium for 100 ns. We analysed the root mean square deviation, fluctuations, and simulative interactions among the protein, ligand, water molecules, and protein-ligand complexes. Most complexes have shown a deviation of <2 Å as cumulative understanding. Also, the fluctuations were lesser, and only a few residues showed the fluctuation with a huge web of interaction between the protein and ligand, providing an edge that supports that the protein and ligand complexes were stable. In the MTT-based Cell Viability Assay, Tiaprofenic Acid exhibited concentration-dependent anti-cancer efficacy against A549 lung cancer cells, significantly reducing viability at 100 μg/mL. These findings highlight its potential as a therapeutic candidate, urging further exploration into the underlying molecular mechanisms for lung cancer treatment.
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Affiliation(s)
- Shaban Ahmad
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Nagmi Bano
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India; Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
| | - Kushagra Khanna
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia.
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
| | - Khalid Raza
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
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2
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Almasoudi HH, Mashraqi MM, Alshamrani S, Alsalmi O, Alharthi AA, Gharib AF. Molecular screening reveals Variolin B as a multitargeted inhibitor of lung cancer: a molecular docking-based fingerprinting and molecular dynamics simulation study. J Biomol Struct Dyn 2024; 42:11-21. [PMID: 37771142 DOI: 10.1080/07391102.2023.2263560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/18/2023] [Indexed: 09/30/2023]
Abstract
Lung Cancer is the topmost death causing cancer and results from smoking, air pollution, cigar, exposure to asbestos or radon-like substances, and genetic factors. The cases of Lung Cancer in south Asian developing nations are being seen most due to heavy pollution and unbalanced lifestyle and putting a considerable burden on healthcare systems. The Food and Drug Administration of the USA has approved almost 100 drugs against SCLC and NSLC and a few drugs that are given to minimise the side effect of anticancer drugs. However, the drugs are shown to be resistant at significantly higher stages and non-affective on cancerous cells and have long-term side effects due to designing the drug by keeping one protein/gene target while designing or repurposing the drugs. In this study, we have taken five main lung cancer protein targets- Nerve growth factor protein (1SG1), Apoptosis inhibitor survivin (1XOX), Heat shock protein (3IUC), Protein tyrosine phosphate (3ZM3), Aldo-keto reductase (4XZL) and screened the complete prepared Drug Bank library of 155888 compounds and identified Variolin B (DB08694) as a multitargeted inhibitor against lung cancer using HTVS, SP and XP sampling algorithms followed by MM\GBSA calculation to sort the best pose. Variolin B is a natural marine antitumor and antiviral compound, so we analysed the ADMET properties and interaction patterns and then simulated all five P-L complexes for 100 ns in water using the NPT ensemble to check its selves against lung cancer. The docking results, ADMET and fingerprints have shown a good performance, and RMSD and RMSF results were with least deviation and fluctuations (<2Å) and produced a huge contact with other residues making the complex stable. The complexes initially fluctuated and deviated due to changes in the solute medium and sudden heat and stabilise after a few ns. However, extensive experimental validation is required before human use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Kingdom of Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Kingdom of Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Kingdom of Saudi Arabia
| | - Ohud Alsalmi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Kingdom of Saudi Arabia
| | - Afaf Awwadh Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Kingdom of Saudi Arabia
| | - Amal F Gharib
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Kingdom of Saudi Arabia
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3
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Saldívar-González FI, Navarrete-Vázquez G, Medina-Franco JL. Design of a multi-target focused library for antidiabetic targets using a comprehensive set of chemical transformation rules. Front Pharmacol 2023; 14:1276444. [PMID: 38027021 PMCID: PMC10651762 DOI: 10.3389/fphar.2023.1276444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Virtual small molecule libraries are valuable resources for identifying bioactive compounds in virtual screening campaigns and improving the quality of libraries in terms of physicochemical properties, complexity, and structural diversity. In this context, the computational-aided design of libraries focused against antidiabetic targets can provide novel alternatives for treating type II diabetes mellitus (T2DM). In this work, we integrated the information generated to date on compounds with antidiabetic activity, advances in computational methods, and knowledge of chemical transformations available in the literature to design multi-target compound libraries focused on T2DM. We evaluated the novelty and diversity of the newly generated library by comparing it with antidiabetic compounds approved for clinical use, natural products, and multi-target compounds tested in vivo in experimental antidiabetic models. The designed libraries are freely available and are a valuable starting point for drug design, chemical synthesis, and biological evaluation or further computational filtering. Also, the compendium of 280 transformation rules identified in a medicinal chemistry context is made available in the linear notation SMIRKS for use in other chemical library enumeration or hit optimization approaches.
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Affiliation(s)
- Fernanda I. Saldívar-González
- Department of Pharmacy, DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - José L. Medina-Franco
- Department of Pharmacy, DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Minetti CA, Remeta DP. Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:1438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying "magic bullets" amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand-target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural-energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Affiliation(s)
- Conceição A. Minetti
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David P. Remeta
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
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Perspective on the Structural Basis for Human Aldo-Keto Reductase 1B10 Inhibition. Metabolites 2021; 11:metabo11120865. [PMID: 34940623 PMCID: PMC8708191 DOI: 10.3390/metabo11120865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Human aldo-keto reductase 1B10 (AKR1B10) is overexpressed in many cancer types and is involved in chemoresistance. This makes AKR1B10 to be an interesting drug target and thus many enzyme inhibitors have been investigated. High-resolution crystallographic structures of AKR1B10 with various reversible inhibitors were deeply analyzed and compared to those of analogous complexes with aldose reductase (AR). In both enzymes, the active site included an anion-binding pocket and, in some cases, inhibitor binding caused the opening of a transient specificity pocket. Different structural conformers were revealed upon inhibitor binding, emphasizing the importance of the highly variable loops, which participate in the transient opening of additional binding subpockets. Two key differences between AKR1B10 and AR were observed regarding the role of external loops in inhibitor binding. The first corresponded to the alternative conformation of Trp112 (Trp111 in AR). The second difference dealt with loop A mobility, which defined a larger and more loosely packed subpocket in AKR1B10. From this analysis, the general features that a selective AKR1B10 inhibitor should comply with are the following: an anchoring moiety to the anion-binding pocket, keeping Trp112 in its native conformation (AKR1B10-like), and not opening the specificity pocket in AR.
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Shao X, Wu J, Yu S, Zhou Y, Zhou C. AKR1B10 inhibits the proliferation and migration of gastric cancer via regulating epithelial-mesenchymal transition. Aging (Albany NY) 2021; 13:22298-22314. [PMID: 34552036 PMCID: PMC8507292 DOI: 10.18632/aging.203538] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/07/2021] [Indexed: 04/13/2023]
Abstract
Gastric cancer (GC) is a common malignancy around the world with a poor prognosis. Aldo-keto reductase family 1 member B10 (AKR1B10) is indispensable to cancer development and progression, which has served as a diagnostic biomarker for tumors. In our study, we demonstrated that the expression of AKR1B10 in GC tissues was significantly lower compared with normal gastric tissues. Subgroup analysis showed that, according to the clinic-pathological factors, the effect of the AKR1B10 expression level on the prognosis of GC patients was significantly different. Moreover, reduced expression of AKR1B10 promoted the ability of GC cells in proliferation and migration. Furthermore, increased AKR1B10 levels resulted in the opposite trend in vitro. Moreover, AKR1B10 was correlated with epithelial-mesenchymal transition (EMT) in a significant way. In vivo experiment, knockdown of AKR1B10 promoted the growth of tumor, increased Vimentin, and E-cadherin significantly. In summary, AKR1B10 is considered as a tumor suppressor in GC and is a promising therapeutic target.
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Affiliation(s)
- Xinyu Shao
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Jue Wu
- Department of Obstetrics and Gynecology, The Suzhou Dushu Lake Hospital, Suzhou, Jiangsu, China
| | - Shunying Yu
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Yuqing Zhou
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Chunli Zhou
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
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Domínguez-Mendoza EA, Galván-Ciprés Y, Martínez-Miranda J, Miranda-González C, Colín-Lozano B, Hernández-Núñez E, Hernández-Bolio GI, Palomino-Hernández O, Navarrete-Vazquez G. Design, Synthesis, and In Silico Multitarget Pharmacological Simulations of Acid Bioisosteres with a Validated In Vivo Antihyperglycemic Effect. Molecules 2021; 26:799. [PMID: 33557136 PMCID: PMC7913794 DOI: 10.3390/molecules26040799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 01/16/2023] Open
Abstract
Substituted phenylacetic (1-3), phenylpropanoic (4-6), and benzylidenethiazolidine-2,4-dione (7-9) derivatives were designed according to a multitarget unified pharmacophore pattern that has shown robust antidiabetic activity. This bioactivity is due to the simultaneous polypharmacological stimulation of receptors PPARα, PPARγ, and GPR40 and the enzyme inhibition of aldose reductase (AR) and protein tyrosine phosphatase 1B (PTP-1B). The nine compounds share the same four pharmacophore elements: an acid moiety, an aromatic ring, a bulky hydrophobic group, and a flexible linker between the latter two elements. Addition and substitution reactions were performed to obtain molecules at moderated yields. In silico pharmacological consensus analysis (PHACA) was conducted to determine their possible modes of action, protein affinities, toxicological activities, and drug-like properties. The results were combined with in vivo assays to evaluate the ability of these compounds to decrease glucose levels in diabetic mice at a 100 mg/kg single dose. Compounds 6 (a phenylpropanoic acid derivative) and 9 (a benzylidenethiazolidine-2,4-dione derivative) ameliorated the hyperglycemic peak in a statically significant manner in a mouse model of type 2 diabetes. Finally, molecular dynamics simulations were executed on the top performing compounds to shed light on their mechanism of action. The simulations showed the flexible nature of the binding pocket of AR, and showed that both compounds remained bound during the simulation time, although not sharing the same binding mode. In conclusion, we designed nine acid bioisosteres with robust in vivo antihyperglycemic activity that were predicted to have favorable pharmacokinetic and toxicological profiles. Together, these findings provide evidence that supports the molecular design we employed, where the unified pharmacophores possess a strong antidiabetic action due to their multitarget activation.
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Affiliation(s)
- Elix Alberto Domínguez-Mendoza
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (E.A.D.-M.); (Y.G.-C.); (J.M.-M.); (C.M.-G.); (B.C.-L.)
| | - Yelzyn Galván-Ciprés
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (E.A.D.-M.); (Y.G.-C.); (J.M.-M.); (C.M.-G.); (B.C.-L.)
| | - Josué Martínez-Miranda
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (E.A.D.-M.); (Y.G.-C.); (J.M.-M.); (C.M.-G.); (B.C.-L.)
| | - Cristian Miranda-González
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (E.A.D.-M.); (Y.G.-C.); (J.M.-M.); (C.M.-G.); (B.C.-L.)
| | - Blanca Colín-Lozano
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (E.A.D.-M.); (Y.G.-C.); (J.M.-M.); (C.M.-G.); (B.C.-L.)
| | - Emanuel Hernández-Núñez
- Cátedra CONACyT, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados, IPN, Unidad Mérida, Yucatan 97310, Mexico; (E.H.-N.); (G.I.H.-B.)
| | - Gloria I. Hernández-Bolio
- Cátedra CONACyT, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados, IPN, Unidad Mérida, Yucatan 97310, Mexico; (E.H.-N.); (G.I.H.-B.)
| | - Oscar Palomino-Hernández
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Juelich, 52425 Julich, Germany;
- Department of Chemistry, Rheinisch-Westfälische Technische Hochschule Aachen, 52425 Aachen, Germany
| | - Gabriel Navarrete-Vazquez
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (E.A.D.-M.); (Y.G.-C.); (J.M.-M.); (C.M.-G.); (B.C.-L.)
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8
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Efficacy of aldose reductase inhibitors is affected by oxidative stress induced under X-ray irradiation. Sci Rep 2019; 9:3177. [PMID: 30816220 PMCID: PMC6395642 DOI: 10.1038/s41598-019-39722-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/29/2019] [Indexed: 01/01/2023] Open
Abstract
Human aldose reductase (hAR, AKR1B1) has been explored as drug target since the 1980s for its implication in diabetic complications. An activated form of hAR was found in cells from diabetic patients, showing a reduced sensitivity to inhibitors in clinical trials, which may prevent its pharmacological use. Here we report the conversion of native hAR to its activated form by X-ray irradiation simulating oxidative stress conditions. Upon irradiation, the enzyme activity increases moderately and the potency of several hAR inhibitors decay before global protein radiation damage appears. The catalytic behavior of activated hAR is also reproduced as the KM increases dramatically while the kcat is not much affected. Consistently, the catalytic tetrad is not showing any modification. The only catalytically-relevant structural difference observed is the conversion of residue Cys298 to serine and alanine. A mechanism involving electron capture is suggested for the hAR activation. We propose that hAR inhibitors should not be designed against the native protein but against the activated form as obtained from X-ray irradiation. Furthermore, since the reactive species produced under irradiation conditions are the same as those produced under oxidative stress, the described irradiation method can be applied to other relevant proteins under oxidative stress environments.
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Ruiz FX, Crespo I, Álvarez S, Porté S, Giménez-Dejoz J, Cousido-Siah A, Mitschler A, de Lera ÁR, Parés X, Podjarny A, Farrés J. Structural basis for the inhibition of AKR1B10 by the C3 brominated TTNPB derivative UVI2008. Chem Biol Interact 2017; 276:174-181. [DOI: 10.1016/j.cbi.2017.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/02/2017] [Accepted: 01/30/2017] [Indexed: 10/20/2022]
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10
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Crystal structures, binding interactions, and ADME evaluation of brain penetrant N -substituted indazole-5-carboxamides as subnanomolar, selective monoamine oxidase B and dual MAO-A/B inhibitors. Eur J Med Chem 2017; 127:470-492. [DOI: 10.1016/j.ejmech.2017.01.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/21/2016] [Accepted: 01/08/2017] [Indexed: 12/20/2022]
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Huang L, He R, Luo W, Zhu YS, Li J, Tan T, Zhang X, Hu Z, Luo D. Aldo-Keto Reductase Family 1 Member B10 Inhibitors: Potential Drugs for Cancer Treatment. Recent Pat Anticancer Drug Discov 2017; 11:184-96. [PMID: 26844556 PMCID: PMC5403964 DOI: 10.2174/1574892811888160304113346] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 01/11/2023]
Abstract
Cytosolic NADPH-dependent reductase AKR1B10 is a member of the aldo-keto reductase (AKR) superfamily. This enzyme is normally expressed in the gastrointestinal tract. However, it is overexpressed in many solid tumors, such as hepatocarcinoma, lung cancer and breast cancer. AKR1B10 may play a role in the formation and development of carcinomas through multiple mechanisms including detoxification of cytotoxic carbonyls, modulation of retinoic acid level, and regulation of cellular fatty acid synthesis and lipid metabolism. Studies have suggested that AKR1B10 may be a useful biomarker for cancer diagnosis and a potential target for cancer treatment. Over the last decade, a number of AKR1B10 inhibitors including aldose reductase inhibitors (ARIs), endogenous substances, natural-based derivatives and synthetic compounds have been developed, which could be novel anticancer drugs. This review provides an overview on related articles and patents about AKR1B10 inhibitors, with a focus on their inhibition selectivity and mechanism of function.
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Affiliation(s)
| | | | | | | | | | | | | | - Zheng Hu
- Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Postdoctoral Mobile Stations of Central South University, Affiliated the First Peoples Hospital of Chenzhou of University of South China, Chenzhou 432000, P.R.China.
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12
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Cousido-Siah A, Ruiz FX, Fanfrlík J, Giménez-Dejoz J, Mitschler A, Kamlar M, Veselý J, Ajani H, Parés X, Farrés J, Hobza P, Podjarny AD. IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors. ACS Chem Biol 2016; 11:2693-2705. [PMID: 27359042 DOI: 10.1021/acschembio.6b00382] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human enzyme aldo-keto reductase family member 1B10 (AKR1B10) has evolved as a tumor marker and promising antineoplastic target. It shares high structural similarity with the diabetes target enzyme aldose reductase (AR). Starting from the potent AR inhibitor IDD388, we have synthesized a series of derivatives bearing the same halophenoxyacetic acid moiety with an increasing number of bromine (Br) atoms on its aryl moiety. Next, by means of IC50 measurements, X-ray crystallography, WaterMap analysis, and advanced binding free energy calculations with a quantum-mechanical (QM) approach, we have studied their structure-activity relationship (SAR) against both enzymes. The introduction of Br substituents decreases AR inhibition potency but improves it in the case of AKR1B10. Indeed, the Br atoms in ortho position may impede these drugs to fit into the AR prototypical specificity pocket. For AKR1B10, the smaller aryl moieties of MK181 and IDD388 can bind into the external loop A subpocket. Instead, the bulkier MK184, MK319, and MK204 open an inner specificity pocket in AKR1B10 characterized by a π-π stacking interaction of their aryl moieties and Trp112 side chain in the native conformation (not possible in AR). Among the three compounds, only MK204 can make a strong halogen bond with the protein (-4.4 kcal/mol, using QM calculations), while presenting the lowest desolvation cost among all the series, translated into the most selective and inhibitory potency AKR1B10 (IC50 = 80 nM). Overall, SAR of these IDD388 polyhalogenated derivatives have unveiled several distinctive AKR1B10 features (shape, flexibility, hydration) that can be exploited to design novel types of AKR1B10 selective drugs.
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Affiliation(s)
- Alexandra Cousido-Siah
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
| | - Francesc X. Ruiz
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Joan Giménez-Dejoz
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - André Mitschler
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
| | - Martin Kamlar
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Jan Veselý
- Department
of Organic Chemistry, Charles University in Prague, Hlavova 2030, 128 43 Prague 2, Czech Republic
| | - Haresh Ajani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Xavier Parés
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department
of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Alberto D. Podjarny
- Department
of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS, 1
rue Laurent Fries 67404 CEDEX Illkirch, France
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