101
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Junior NN, Santos IA, Meireles BA, Nicolau MSP, Lapa IR, Aguiar RS, Jardim ACG, José DP. In silico evaluation of lapachol derivatives binding to the Nsp9 of SARS-CoV-2. J Biomol Struct Dyn 2021; 40:5917-5931. [PMID: 33478342 PMCID: PMC7832454 DOI: 10.1080/07391102.2021.1875050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
SARS-CoV-2 is the etiological agent of COVID-19, which represents a global health emergency that was rapidly declared a pandemic by the World Health Organization. Currently, there is a dearth of effective targeted therapies against viruses. Natural products isolated from traditional herbal plants have had a huge impact on drug development aimed at various diseases. Lapachol is a 1,4- naphthoquinone compound that has been demonstrated to have therapeutic effects against several diseases. SARS-CoV-2 non-structural proteins (nsps) play an important role in the viral replication cycle. Nsp9 seems to play a key role in transcription of the RNA genome of SARS-CoV-2. Virtual screening by docking and molecular dynamics suggests that lapachol derivatives can interact with Nsp9 from SARS-CoV-2. Complexes of lapachol derivatives V, VI, VIII, IX, and XI with the Nsp9 RNA binding site were subjected to molecular dynamics assays, to assess the stability of the complexes via RMSD. All complexes were stable over the course of 100 ns dynamics assays. Analyses of the hydrogen bonds in the complexes showed that lapachol derivatives VI and IX demonstrated strongest binding, with a stable or increasing number of hydrogen bonds over time. Our results demonstrate that Nsp9 from SARS-CoV-2 could be an important target in prospecting for ligands with antiviral potential. In addition, we showed that lapachol derivatives are potential ligands for SARS-CoV-2 Nsp9. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Nilson Nicolau Junior
- Laboratory of Molecular Modeling, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil
| | - Igor Andrade Santos
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bruno Amaral Meireles
- Campus Universitário de Iturama, Federal University of Triângulo Mineiro, Iturama, MG, Brazil
| | | | - Igor Rodrigues Lapa
- Campus Universitário de Iturama, Federal University of Triângulo Mineiro, Iturama, MG, Brazil
| | - Renato Santana Aguiar
- Laboratory of Integrative Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Virology, Institute of Biomedical Science, ICBIM, Federal University of Uberlândia, Uberlândia, Brazil
| | - Diego Pandeló José
- Campus Universitário de Iturama, Federal University of Triângulo Mineiro, Iturama, MG, Brazil
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102
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Sundriyal S, Eeda V, Lagisetty P, Awasthi V. Tubulin inhibitory activity of a novel colchicine-binding compounds based on a dinaphthospiropyranran scaffold. Bioorg Med Chem 2021; 29:115874. [PMID: 33223461 DOI: 10.1016/j.bmc.2020.115874] [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: 08/24/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022]
Abstract
Spiropyrans have been investigated for their thermo- and photochromic characteristics, but their biotherapeutic properties have not been addressed. We report anti-proliferative properties of a novel dinaphthospiropyran analogue (1). The compound 1 was synthesized by a simple and expedient method using a one-pot acid-catalyzed aldol condensation of 2-hydroxy-1-naphthaldehyde with 4-piperidone followed by an acetalization reaction. Compound 1 was submitted to anticancer drug screen in the National Cancer Institute's panel of 60 human tumor cell lines. The average concentration of 1 to inhibit 50% cell growth was 5.4 ± 0.23 µM. All cell lines responded at almost the same concentration, suggesting that the action of 1 is not selective for cancer of origin. COMPARE analysis of dose-response data revealed interaction with tubulin as the possible mechanism of action of 1. At molecular level, 1 induced tubulin reorganization in colon cancer HCT-116 cells. Under cell-free conditions, the efficacy of 1 to inhibit tubulin polymerization was comparable to that of paclitaxel and vinblastine. Molecular docking showed that compound 1 binds to the colchicine-binding site of tubulin. We conclude that dinaphthospiropyrans present a novel scaffold for the development of tubulin inhibitors.
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Affiliation(s)
- Sandeep Sundriyal
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, 1110 N. Stonewall Avenue, Oklahoma City, OK 73117, USA
| | - Venkateswararao Eeda
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, 1110 N. Stonewall Avenue, Oklahoma City, OK 73117, USA
| | - Pallavi Lagisetty
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, 1110 N. Stonewall Avenue, Oklahoma City, OK 73117, USA
| | - Vibhudutta Awasthi
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, 1110 N. Stonewall Avenue, Oklahoma City, OK 73117, USA.
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103
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Sciortino G, Maréchal JD, Garribba E. Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01507e] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.
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Affiliation(s)
- Giuseppe Sciortino
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Jean-Didier Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia
- Università di Sassari
- 07100 Sassari
- Italy
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104
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Deciphering the role of sulfonamides and molecular basis of thioredoxin domain dynamics through comparative simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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105
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First Synthesis of Racemic Trans Propargylamino-Donepezil, a Pleiotrope Agent Able to Both Inhibit AChE and MAO-B, with Potential Interest against Alzheimer's Disease. Molecules 2020; 26:molecules26010080. [PMID: 33375412 PMCID: PMC7795340 DOI: 10.3390/molecules26010080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023] Open
Abstract
Alzheimer’s disease (AD) is a multifactorial neurodegenerative disease towards which pleiotropic approach using Multi-Target Directed Ligands is nowadays recognized as probably convenient. Among the numerous targets which are today validated against AD, acetylcholinesterase (ACh) and Monoamine Oxidase-B (MAO-B) appear as particularly convincing, especially if displayed by a sole agent such as ladostigil, currently in clinical trial in AD. Considering these results, we wanted to take benefit of the structural analogy lying in donepezil (DPZ) and rasagiline, two indane derivatives marketed as AChE and MAO-B inhibitors, respectively, and to propose the synthesis and the preliminary in vitro biological characterization of a structural compromise between these two compounds, we called propargylaminodonepezil (PADPZ). The synthesis of racemic trans PADPZ was achieved and its biological evaluation established its inhibitory activities towards both (h)AChE (IC50 = 0.4 µM) and (h)MAO-B (IC50 = 6.4 µM).
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106
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Sánchez-Aparicio JE, Tiessler-Sala L, Velasco-Carneros L, Roldán-Martín L, Sciortino G, Maréchal JD. BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization. J Chem Inf Model 2020; 61:311-323. [PMID: 33337144 DOI: 10.1021/acs.jcim.0c00827] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With a large amount of research dedicated to decoding how metallic species bind to proteins, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal-binding templates. These approaches are fundamentally focused on the first coordination sphere of the metal. Here, we present the BioMetAll predictor that is based on a different postulate: the formation of a potential metal-binding site is related to the geometric organization of the protein backbone. We first report the set of convenient geometric descriptors of the backbone needed for the algorithm and their parameterization from a statistical analysis. Then, the successful benchmark of BioMetAll on a set of more than 90 metal-binding X-ray structures is presented. Because BioMetAll allows structural predictions regardless of the exact geometry of the side chains, it appears extremely valuable for systems whose structures (either experimental or theoretical) are not optimal for metal-binding sites. We report here its application on three different challenging cases: (i) the modulation of metal-binding sites during conformational transition in human serum albumin, (ii) the identification of possible routes of metal migration in hemocyanins, and (iii) the prediction of mutations to generate convenient metal-binding sites for de novo biocatalysts. This study shows that BioMetAll offers a versatile platform for numerous fields of research at the interface between inorganic chemistry and biology and allows to highlight the role of the preorganization of the protein backbone as a marker for metal binding. BioMetAll is an open-source application available at https://github.com/insilichem/biometall.
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Affiliation(s)
- José-Emilio Sánchez-Aparicio
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Laura Tiessler-Sala
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Lorea Velasco-Carneros
- Biofisika Institute (UPV/EHU, CSIC) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Lorena Roldán-Martín
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
| | - Giuseppe Sciortino
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdanyola del Vallés, Barcelona, Spain
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107
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Huddle BC, Grimley E, Chtcherbinine M, Buchman CD, Takahashi C, Debnath B, McGonigal SC, Mao S, Li S, Felton J, Pan S, Wen B, Sun D, Neamati N, Buckanovich RJ, Hurley TD, Larsen SD. Development of 2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one inhibitors of aldehyde dehydrogenase 1A (ALDH1A) as potential adjuncts to ovarian cancer chemotherapy. Eur J Med Chem 2020; 211:113060. [PMID: 33341649 DOI: 10.1016/j.ejmech.2020.113060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
There is strong evidence that inhibition of one or more Aldehyde Dehydrogenase 1A (ALDH1A) isoforms may be beneficial in chemotherapy-resistant ovarian cancer and other tumor types. While many previous efforts have focused on development of ALDH1A1 selective inhibitors, the most deadly ovarian cancer subtype, high-grade serous (HGSOC), exhibits elevated expression of ALDH1A3. Herein, we report continued development of pan-ALDH1A inhibitors to assess whether broad spectrum ALDH1A inhibition is an effective adjunct to chemotherapy in this critical tumor subtype. Optimization of the CM39 scaffold, aided by metabolite ID and several new ALDH1A1 crystal structures, led to improved biochemical potencies, improved cellular ALDH inhibition in HGSOC cell lines, and substantial improvements in microsomal stability culminating in orally bioavailable compounds. We demonstrate that two compounds 68 and 69 are able to synergize with chemotherapy in a resistant cell line and patient-derived HGSOC tumor spheroids, indicating their suitability for future in vivo proof of concept experiments.
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Affiliation(s)
- Brandt C Huddle
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Edward Grimley
- Division of Hematology-Oncology, Departments of Internal Medicine and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh Medical Center and the Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Mikhail Chtcherbinine
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Cameron D Buchman
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Cyrus Takahashi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Bikash Debnath
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Stacy C McGonigal
- Division of Hematology-Oncology, Departments of Internal Medicine and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh Medical Center and the Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Shuai Mao
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Siwei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeremy Felton
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shu Pan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ronald J Buckanovich
- Division of Hematology-Oncology, Departments of Internal Medicine and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh Medical Center and the Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Thomas D Hurley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Scott D Larsen
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA.
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108
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Toublet FX, Lalut J, Hatat B, Lecoutey C, Davis A, Since M, Corvaisier S, Freret T, Sopková-de Oliveira Santos J, Claeysen S, Boulouard M, Dallemagne P, Rochais C. Pleiotropic prodrugs: Design of a dual butyrylcholinesterase inhibitor and 5-HT 6 receptor antagonist with therapeutic interest in Alzheimer's disease. Eur J Med Chem 2020; 210:113059. [PMID: 33310288 DOI: 10.1016/j.ejmech.2020.113059] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/23/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022]
Abstract
Beside acetylcholinesterase, butyrylcholinesterase could be considered as a putative target of interest for the symptomatic treatment of Alzheimer's disease (AD). As a result of complexity of AD, no molecule has been approved since 2002. Idalopirdine, a 5-HT6 receptors antagonist, did not show its effectiveness in clinical trial despite its evaluation as adjunct to cholinesterase inhibitors. Pleiotropic molecules, known as multitarget directed ligands (MTDLs) are currently developed to tackle the multifactorial origin of AD. In this context, we have developed a pleiotropic carbamate 7, that behaves as a covalent inhibitor of BuChE (IC50 = 0.97 μM). The latter will deliver after hydrolysis, compound 6, a potent 5-HT6 receptors antagonist (Ki = 11.4 nM) related to idalopirdine. In silico and in vitro evaluation proving our concept were performed completed with first in vivo results that demonstrate great promise in restoring working memory.
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Affiliation(s)
| | - Julien Lalut
- Normandie Univ, Unicaen, CERMN, 14000 Caen, France
| | - Bérénice Hatat
- Normandie Univ, Unicaen, CERMN, 14000 Caen, France; IGF, Univ. Montpellier, CNRS, INSERM Montpellier, France
| | | | - Audrey Davis
- Normandie Univ, Unicaen, CERMN, 14000 Caen, France
| | - Marc Since
- Normandie Univ, Unicaen, CERMN, 14000 Caen, France
| | | | - Thomas Freret
- Normandie Univ, Unicaen, INSERM, Comete, GIP CYCERON, 14000 Caen, France
| | | | | | - Michel Boulouard
- Normandie Univ, Unicaen, INSERM, Comete, GIP CYCERON, 14000 Caen, France
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109
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Quorum quenching by 2-Hydroxyanisole extracted from Solanum torvum on Pseudomonas aeruginosa and its inhibitory action upon LasR protein. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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110
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Li Y, Sun H, Tian Z, Su X, Li Y, Ye X, Zhou Y, Zheng S, Liu J, Zhang Y. The determination of Plutella xylostella (L.) GSTs (PxGSTs) involved in the detoxification metabolism of Tolfenpyrad. PEST MANAGEMENT SCIENCE 2020; 76:4036-4045. [PMID: 32515133 DOI: 10.1002/ps.5958] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Insect glutathione S-transferases (GSTs) play a crucial role in insecticide detoxification. However, there remains a distinct lack of information regarding the role of GSTs in the detoxification of Tolfenpyrad (TFP) in insects. RESULTS Real-time quantitative PCR showed significant upregulation of PxGSTs after exposure to TFP for 6 h. An in vitro inhibition assay showed that TFP could inhibit PxGSTδ, PxGSTε and PxGSTσ, and the most pronounced inhibitory effect was on PxGSTσ. Metabolism assays displayed that PxGSTσ was superior to other test PxGSTs in metabolizing TFP. The molecular docking of TFP and PxGSTσ revealed that the H-bond provided by the sidechains of Tyr107 and Tyr162 were key to the detoxification of TFP by PxGSTσ. Further tests using mutant PxGSTσ proteins at the sites of Tyr107 (PxGSTσY107A) and Tyr162 (PxGSTσY162A) corroborated that the individual replacement of Tyr107 and Tyr162 could greatly weaken the binding and metabolic abilities to TFP. CONCLUSION Metabolic interactions between the Plutella xylostella (L.) GSTs (PxGSTs) and TFP were deciphered. This study illustrates the molecular metabolism mechanism of PxGSTσ towards TFP and provides theoretical underpinnings for the design and optimization of novel TFP-like insecticides. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Yifan Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Hong Sun
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zhen Tian
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xinxin Su
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yue Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xuan Ye
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yifei Zhou
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Shengli Zheng
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China
| | - Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
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111
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Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine. Sci Rep 2020; 10:20709. [PMID: 33244063 PMCID: PMC7691350 DOI: 10.1038/s41598-020-77377-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/10/2020] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a d-alanine-d-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to d-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and d-cycloserine binding pockets of Ddl.
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112
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Neubauer PR, Pienkny S, Wessjohann L, Brandt W, Sewald N. Predicting the Substrate Scope of the Flavin-Dependent Halogenase BrvH. Chembiochem 2020; 21:3282-3288. [PMID: 32645255 PMCID: PMC7754283 DOI: 10.1002/cbic.202000444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 01/16/2023]
Abstract
The recently described flavin-dependent halogenase BrvH is able to catalyse both the bromination and chlorination of indole, but shows significantly higher bromination activity. BrvH was annotated as a tryptophan halogenase, but does not accept tryptophan as a substrate. Its native substrate remains unknown. A predictive model with the data available for BrvH was analysed. A training set of compounds tested in vitro was docked into the active site of a complete protein model based on the X-ray structure of BrvH. The atoms not resolved experimentally were modelled by using molecular mechanics force fields to obtain this protein model. Furthermore, docking poses for the substrates and known non-substrates have been calculated. Parameters like distance, partial charge and hybridization state were analysed to derive rules for predicting activity. With this model for activity of the BrvH, a virtual screening suggested several structures for potential substrates. Some of the compounds preselected in this way were tested in vitro, and several could be verified as convertible substrates. Based on information on halogenated natural products, a new dataset was created to specifically search for natural products as substrates/products, and virtual screening in this database yielded further hits.
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Affiliation(s)
- Pia R. Neubauer
- Organic and Bioorganic ChemistryDepartment of ChemistryBielefeld UniversityUniversitätsstrasse 2533501BielefeldGermany
| | - Silke Pienkny
- Leibniz Institute for Plant Biochemistry (IPB)Weinberg 306120HalleGermany
| | - Ludger Wessjohann
- Leibniz Institute for Plant Biochemistry (IPB)Weinberg 306120HalleGermany
| | - Wolfgang Brandt
- Leibniz Institute for Plant Biochemistry (IPB)Weinberg 306120HalleGermany
| | - Norbert Sewald
- Organic and Bioorganic ChemistryDepartment of ChemistryBielefeld UniversityUniversitätsstrasse 2533501BielefeldGermany
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113
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Computational studies on cholinesterases: Strengthening our understanding of the integration of structure, dynamics and function. Neuropharmacology 2020; 179:108265. [DOI: 10.1016/j.neuropharm.2020.108265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/21/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022]
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114
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From pan-genome to protein dynamics: A computational hierarchical quest to identify drug target in multi-drug resistant Burkholderia cepacia. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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115
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Mandour YM, Zlotos DP, Alaraby Salem M. A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease. J Biomol Struct Dyn 2020; 40:2327-2338. [PMID: 33094680 PMCID: PMC7597227 DOI: 10.1080/07391102.2020.1837680] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to quickly identify promising drug candidates. SARS-CoV-2 main protease (Mpro) is responsible for the maturation of viral functional proteins making it a key antiviral target. Based on the recently revealed crystal structures of SARS-CoV-2 Mpro, we herein describe a multi-stage virtual screening protocol including pharmacophore screening, molecular docking and protein-ligand interaction fingerprints (PLIF) post-docking filtration for efficient enrichment of potent SARS-CoV-2 Mpro inhibitors. Potential hits, along with a cocrystallized control were further studied via molecular dynamics. A 150-ns production trajectory was followed by RMSD, free energy calculation, and H-bond analysis for each compound. The applied virtual screening protocol led to identification of five FDA-approved drugs with promising binding modes to key subsites of the substrate-binding pocket of SARS-CoV-2 Mpro. The identified compounds belong to different pharmaceutical classes, including several protease inhibitors, antineoplastic agents and a natural flavonoid. The drug candidates discovered in this study present a potential extension of the recently reported SARS-CoV-2 Mpro inhibitors that have been identified using other virtual screening protocols and may be repurposed for COVID-19 treatment.
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Affiliation(s)
- Yasmine M Mandour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, Cairo, Egypt.,School of Life and Medical Sciences, University of Hertfordshire hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt
| | - Darius P Zlotos
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, Cairo, Egypt
| | - M Alaraby Salem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, October University of Modern Sciences and Arts (MSA), Giza, Egypt
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116
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Uysal S, Soyer Z, Saylam M, Tarikogullari AH, Yilmaz S, Kirmizibayrak PB. Design, synthesis and biological evaluation of novel naphthoquinone-4-aminobenzensulfonamide/carboxamide derivatives as proteasome inhibitors. Eur J Med Chem 2020; 209:112890. [PMID: 33039723 DOI: 10.1016/j.ejmech.2020.112890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 10/23/2022]
Abstract
A series of novel 4-aminobenzensulfonamide/carboxamide derivatives bearing naphthoquinone pharmacophore were designed, sythesized and evaluated for their proteasome inhibitory and antiproliferative activities against human breast cancer cell line (MCF-7). The structures of the synthesized compounds were confirmed by spectral and elemental analyses. The proteasome inhibitory activity studies were carried out using cell-based assay. The antiproteasomal activity results revealed that most of the compounds exhibited inhibitory activity with different percentages against the caspase-like (C-L, β1 subunit), trypsin-like (T-L, β2 subunit) and chymotrypsin-like (ChT-L, β5 subunit) activities of proteasome. Among the tested compounds, compound 14 bearing 5-chloro-2-pyridyl ring on the nitrogen atom of sulfonamide group is the most active compound in the series and displayed higher inhibition with IC50 values of 9.90 ± 0.61, 44.83 ± 4.23 and 22.27 ± 0.15 μM against ChT-L, C-L and T-L activities of proteasome compared to the lead compound PI-083 (IC50 = 12.47 ± 0.21, 53.12 ± 2.56 and 26.37 ± 0.5 μM), respectively. The antiproliferative activity was also determined by MTT (3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide) assay in vitro. According to the antiproliferative activity results, all of the compounds exhibited cell growth inhibitory activity in a range of IC50 = 1.72 ± 0.14-20.8 ± 0.5 μM and compounds 13 and 28 were found to be the most active compounds with IC50 values of 1.79 ± 0.21 and 1.72 ± 0.14 μM, respectively. Furthermore, molecular modeling studies were carried out for the compounds 13, 14 and 28 to investigate the ligand-enzyme binding interactions.
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Affiliation(s)
- Sirin Uysal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, İzmir, Turkey
| | - Zeynep Soyer
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, İzmir, Turkey.
| | - Merve Saylam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, İzmir Katip Celebi University, İzmir, Turkey
| | - Ayse H Tarikogullari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, İzmir, Turkey
| | - Sinem Yilmaz
- Department of Biotechnology, Institute of Science, Ege University, İzmir, Turkey; Department of Bioengineering, Faculty of Engineering, University of Alaaddin Keykubat, Antalya, Turkey
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117
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Ren S, de Kok NAW, Gu Y, Yan W, Sun Q, Chen Y, He J, Tian L, Andringa RLH, Zhu X, Tang M, Qi S, Xu H, Ren H, Fu X, Minnaard AJ, Yang S, Zhang W, Li W, Wei Y, Driessen AJM, Cheng W. Structural and Functional Insights into an Archaeal Lipid Synthase. Cell Rep 2020; 33:108294. [PMID: 33086053 DOI: 10.1016/j.celrep.2020.108294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/27/2020] [Accepted: 09/30/2020] [Indexed: 02/08/2023] Open
Abstract
The UbiA superfamily of intramembrane prenyltransferases catalyzes an isoprenyl transfer reaction in the biosynthesis of lipophilic compounds involved in cellular physiological processes. Digeranylgeranylglyceryl phosphate (DGGGP) synthase (DGGGPase) generates unique membrane core lipids for the formation of the ether bond between the glycerol moiety and the alkyl chains in archaea and has been confirmed to be a member of the UbiA superfamily. Here, the crystal structure is reported to exhibit nine transmembrane helices along with a large lateral opening covered by a cytosolic cap domain and a unique substrate-binding central cavity. Notably, the lipid-bound states of this enzyme demonstrate that the putative substrate-binding pocket is occupied by the lipidic molecules used for crystallization, indicating the binding mode of hydrophobic substrates. Collectively, these structural and functional studies provide not only an understanding of lipid biosynthesis by substrate-specific lipid-modifying enzymes but also insights into the mechanisms of lipid membrane remodeling and adaptation.
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Affiliation(s)
- Sixue Ren
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Yijun Gu
- National Facility for Protein Science Shanghai, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute (Zhangjiang Lab), Zhangheng Road 239, Shanghai 201203, China
| | - Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qiu Sun
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yunying Chen
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jun He
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lejin Tian
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Ruben L H Andringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Xiaofeng Zhu
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Mei Tang
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shiqian Qi
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Heng Xu
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xianghui Fu
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Shengyong Yang
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Wanjiang Zhang
- Department of Pathophysiology, Shihezi University School of Medicine, the Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi, Xinjiang 832002, China
| | - Weimin Li
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yuquan Wei
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China.
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118
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Yuan XY, Li M, Yu X, Li H. Structural analysis, simulation, and molecular docking of aza-nitrile into cathepsins to explain the high selectivity. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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119
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Yu D, Wu D, Liu JY, Li SY, Li Y. On single-electron magnesium bonding formation and the effect of methyl substitution. RSC Adv 2020; 10:34413-34420. [PMID: 35514394 PMCID: PMC9056782 DOI: 10.1039/d0ra06591a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
The complexes formed between MgX2 (X = F, H) molecules and alkyl radicals Y [Y = CH3, CH2CH3, CH(CH3)2, and C(CH3)3] have been characterized by using quantum chemical methods. The binding distance in all cases is less than the sum of vdW radii of Mg and C, indicating the formation of a non-covalent interaction, namely single-electron magnesium bond. Energy decomposition analysis reveals that electrostatic and polarization contributions are the major components responsible for the stability of the studied complexes. According to interaction energy, atoms in molecules, and independent gradient model analyses, methyl substitution on electron donor Y imposes a positive effect on its complexation with MgX2. When compared with other nonbonded interactions, the single-electron magnesium bond is found to have strength comparable to those of the single-electron beryllium bond and π-magnesium bond. The complexes formed between MgX2 (X = F, H) molecules and alkyl radicals Y [Y = CH3, CH2CH3, CH(CH3)2, and C(CH3)3] have been characterized by using quantum chemical methods.![]()
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Affiliation(s)
- Dan Yu
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
| | - Di Wu
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
| | - Jing-Yao Liu
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
| | - Si-Yi Li
- Department of Transdisciplinary Science and Engineering, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro Tokyo 152-8551 Japan
| | - Ying Li
- Institute of Theoretical Chemistry, Laboratory of Theoretical and Computational Chemistry, College of Chemistry, Jilin University Changchun 130023 P. R. China
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120
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Bellany F, Tsuchiya Y, Tran TM, Chan AWE, Allan H, Gout I, Tabor AB. Design and synthesis of Coenzyme A analogues as Aurora kinase A inhibitors: An exploration of the roles of the pyrophosphate and pantetheine moieties. Bioorg Med Chem 2020; 28:115740. [PMID: 33007553 DOI: 10.1016/j.bmc.2020.115740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022]
Abstract
Coenzyme A (CoA) is a highly selective inhibitor of the mitotic regulatory enzyme Aurora A kinase, with a novel mode of action. Herein we report the design and synthesis of analogues of CoA as inhibitors of Aurora A kinase. We have designed and synthesised modified CoA structures as potential inhibitors, combining dicarbonyl mimics of the pyrophosphate group with a conserved adenosine headgroup and different length pantetheine-based tail groups. An analogue with a -SH group at the end of the pantotheinate tail showed the best IC50, probably due to the formation of a covalent bond with Aurora A kinase Cys290.
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Affiliation(s)
- Fiona Bellany
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK
| | - Yugo Tsuchiya
- Department of Structural and Molecular Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Trang M Tran
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK
| | - A W Edith Chan
- Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Helen Allan
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK
| | - Ivan Gout
- Department of Structural and Molecular Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Alethea B Tabor
- Department of Chemistry, UCL, Christopher Ingold Building, 20, Gordon Street, London WC1H 0AJ, UK.
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121
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Nazar A, Abbas G, Azam SS. Deciphering the Inhibition Mechanism of under Trial Hsp90 Inhibitors and Their Analogues: A Comparative Molecular Dynamics Simulation. J Chem Inf Model 2020; 60:3812-3830. [PMID: 32659088 DOI: 10.1021/acs.jcim.9b01134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Heat shock protein 90 (Hsp90) performs functions in cellular activities together with other signaling pathways. Hsp90 is evolutionarily conserved and universally articulated as a human cancer-causing agent involved in lung cancer and breast cancer followed by colon and rectum cancers. It has emerged as an effective drug candidate, and inhibition may affect several signaling pathways associated with cancer spread. Therefore, in-silico approaches, molecular docking, molecular dynamics simulation, and binding free energy calculations were applied to create insights into the inhibition mechanism against Hsp90 to identify new cancer therapeutic drugs. Top-docked Hsp90-inhibitor complexes with their analogues were selected as the best complexes based on the GOLD fitness score and orientation. The significant interaction of Hsp90 inhibitors and their analogues were observed to be bound with active site residues as well as residing within the same cavity region. System stability factors RMSD, RMSF, beta-factor, and radius of gyration were analyzed for top-docked complexes and ensure strong binding interaction between inhibitors and the Hsp90 cavity. Cavity bound inhibitors were found to retain consistent hydrogen bonding during the simulation. The radial distribution function (RDF) illustrated that interacting active site residues drive the binding and stability of the inhibitors. Similarly, the axial frequency distribution, which is an indigenously developed analytical tool, produced noteworthy knowledge of the hydrogen-bonding pattern. Results yielded new insights into the design of cancer therapeutic drugs against Hsp90. This finding suggests that under trial Hsp90 inhibitors MPC-3100 could be a potential starting point into the development of potential anticancer agents with the possibility of future directions for the improvement of early existing Hsp90 inhibitors CNF-2024 and SNX-5422 as an anticancer agent.
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Affiliation(s)
- Asma Nazar
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Ghulam Abbas
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
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122
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Riva V, Garbelli A, Brai A, Casiraghi F, Fazi R, Trivisani CI, Boccuto A, Saladini F, Vicenti I, Martelli F, Zazzi M, Giannecchini S, Dreassi E, Botta M, Maga G. Unique Domain for a Unique Target: Selective Inhibitors of Host Cell DDX3X to Fight Emerging Viruses. J Med Chem 2020; 63:9876-9887. [PMID: 32787106 DOI: 10.1021/acs.jmedchem.0c01039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Emerging viruses like dengue, West Nile, chikungunya, and Zika can cause widespread viral epidemics. Developing novel drugs or vaccines against specific targets for each virus is a difficult task. As obligate parasites, all viruses exploit common cellular pathways, providing the possibility to develop broad-spectrum antiviral agents targeting host factors. The human DEAD-box RNA helicase DDX3X is an essential cofactor for viral replication but dispensable for cell viability. Herein, we exploited the presence of a unique structural motif of DDX3X not shared by other cellular enzymes to develop a theoretical model to aid in the design of a novel class of highly selective inhibitors acting against such specific targets, thus limiting off-targeting effects. High-throughput virtual screening led us to identify hit compound 5, endowed with promising antienzymatic activity. To improve its aqueous solubility, 5 and its two enantiomers were synthesized and converted into their corresponding acetate salts (compounds 11, 12, and 13). In vitro mutagenesis and biochemical and cellular assays further confirmed that the developed molecules were selective for DDX3X and were able to suppress replication of West Nile and dengue viruses in infected cells in the micromolar range while showing no toxicity for uninfected cells. These results provide proof of principle for a novel strategy in developing highly selective and broad-spectrum antiviral molecules active against emerging and dangerous viral pathogens. This study paves the way for the development of larger focused libraries targeting such domain to expand SAR studies and fully characterize their mode of interaction.
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Affiliation(s)
- Valentina Riva
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Anna Garbelli
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Annalaura Brai
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Federica Casiraghi
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
| | - Roberta Fazi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Claudia I Trivisani
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Adele Boccuto
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Saladini
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Ilaria Vicenti
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Francesco Martelli
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Maurizio Zazzi
- Dipartimento di Biotecnologie Mediche, Università degli Studi di Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Simone Giannecchini
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, Viale Morgnani 48, I-50134 Firenze, Italy
| | - Elena Dreassi
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Maurizio Botta
- Dipartimento Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Biotechnology College of Science and Technology, Temple University, Biolife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Giovanni Maga
- Istituto di Genetica Molecolare IGM-CNR "Luigi Luca Cavalli-Sforza", Via Abbiategrasso 207, I-27100 Pavia, Italy
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123
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Pathaw N, Gurung AB, Chrungoo NK, Bhattacharjee A, Roy SS, Ansari MA, Sharma SK. In silico molecular modelling, structural dynamics simulation and characterization of antifungal nature of β-glucosidase enzyme from Sechium edule. J Biomol Struct Dyn 2020; 39:4501-4509. [PMID: 32666889 DOI: 10.1080/07391102.2020.1791956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
β-glucosidase is an enzyme that has ability to cleave β-glycosidic bonds present in oligosaccharides and glycoconjugates. They are known to be present across all domains of living organism and have important roles in many biological processes including plant defense mechanism. In the present study, a β-glucosidase enzyme identified from seeds of Sechium edule was characterized using various bioinformatics tools. A homology model (SeBG) was generated using a β-glucosidase crystal structure from Oryza sativa (PDB ID: 3PTK) as template. In silico structural binding studies on putative β-glucosidase protein revealed a stable and strong interaction indicative of higher GOLD fitness score with the substrates: p-nitrophenyl-β-d-glucopyranoside (pNPG), laminarin, chitotriose, N-acetylglucosamine and N-acetylmuramic acid suggesting its possible role in broad spectrum antifungal and antimicrobial activity. Assessment of the in vitro enzyme activity with pNPG showed a Km and Vmax values of 2.7 mM and 22 µMmin-1mL-1mg-1, respectively. While, the in vitro enzyme activity with laminarin showed a Km and Vmax values of 0.31 mM and 0.043 µMmin-1mL-1mg-1. The broad spectrum activity of the protein shown in our result indicates SeBG as a promising biocontrol agent against phytopathogens.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neeta Pathaw
- ICAR Research Complex for NEH Region, Lamphelpat, Imphal, Manipur, India
| | - Arun Bahadur Gurung
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, India
| | - Nikhil Kumar Chrungoo
- Centre for Advanced Studies in Botany, North Eastern Hill University, Shillong, India
| | - Atanu Bhattacharjee
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, India
| | - Subhra Saikat Roy
- ICAR Research Complex for NEH Region, Lamphelpat, Imphal, Manipur, India
| | - Meraj Alam Ansari
- ICAR Research Complex for NEH Region, Lamphelpat, Imphal, Manipur, India
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124
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Tessaro F, Scapozza L. How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids? Molecules 2020; 25:E2749. [PMID: 32545835 PMCID: PMC7355999 DOI: 10.3390/molecules25122749] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022] Open
Abstract
In this review, we retraced the '40-year evolution' of molecular docking algorithms. Over the course of the years, their development allowed to progress from the so-called 'rigid-docking' searching methods to the more sophisticated 'semi-flexible' and 'flexible docking' algorithms. Together with the advancement of computing architecture and power, molecular docking's applications also exponentially increased, from a single-ligand binding calculation to large screening and polypharmacology profiles. Recently targeting nucleic acids with small molecules has emerged as a valuable therapeutic strategy especially for cancer treatment, along with bacterial and viral infections. For example, therapeutic intervention at the mRNA level allows to overcome the problematic of undruggable proteins without modifying the genome. Despite the promising therapeutic potential of nucleic acids, molecular docking programs have been optimized mostly for proteins. Here, we have analyzed literature data on nucleic acid to benchmark some of the widely used docking programs. Finally, the comparison between proteins and nucleic acid targets docking highlighted similarity and differences, which are intrinsically related to their chemical and structural nature.
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Affiliation(s)
- Francesca Tessaro
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva CMU, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland;
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry, School of Pharmaceutical Sciences, University of Geneva CMU, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland;
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
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125
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Mora Lagares L, Minovski N, Caballero Alfonso AY, Benfenati E, Wellens S, Culot M, Gosselet F, Novič M. Homology Modeling of the Human P-glycoprotein (ABCB1) and Insights into Ligand Binding through Molecular Docking Studies. Int J Mol Sci 2020; 21:ijms21114058. [PMID: 32517082 PMCID: PMC7312539 DOI: 10.3390/ijms21114058] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
The ABCB1 transporter also known as P-glycoprotein (P-gp) is a transmembrane protein belonging to the ATP binding cassette super-family of transporters; it is a xenobiotic efflux pump that limits intracellular drug accumulation by pumping the compounds out of cells. P-gp contributes to a decrease of toxicity and possesses broad substrate specificity. It is involved in the failure of numerous anticancer and antiviral chemotherapies due to the multidrug resistance (MDR) phenomenon, where it removes the chemotherapeutics out of the targeted cells. Understanding the details of the ligand–P-gp interaction is therefore crucial for the development of drugs that might overcome the MRD phenomenon and for obtaining a more effective prediction of the toxicity of certain compounds. In this work, an in silico modeling was performed using homology modeling and molecular docking methods with the aim of better understanding the ligand–P-gp interactions. Based on different mouse P-gp structural templates from the PDB repository, a 3D model of the human P-gp (hP-gp) was constructed by means of protein homology modeling. The homology model was then used to perform molecular docking calculations on a set of thirteen compounds, including some well-known compounds that interact with P-gp as substrates, inhibitors, or both. The sum of ranking differences (SRD) was employed for the comparison of the different scoring functions used in the docking calculations. A consensus-ranking scheme was employed for the selection of the top-ranked pose for each docked ligand. The docking results showed that a high number of π interactions, mainly π–sigma, π–alkyl, and π–π type of interactions, together with the simultaneous presence of hydrogen bond interactions contribute to the stability of the ligand–protein complex in the binding site. It was also observed that some interacting residues in hP-gp are the same when compared to those observed in a co-crystallized ligand (PBDE-100) with mouse P-gp (PDB ID: 4XWK). Our in silico approach is consistent with available experimental results regarding P-gp efflux transport assay; therefore it could be useful in the prediction of the role of new compounds in systemic toxicity.
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Affiliation(s)
- Liadys Mora Lagares
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-01-476-0253 (L.M.L. & M.N.)
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
| | - Ana Yisel Caballero Alfonso
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche “Mario Negri”—IRCCS, 20156 Milano, Italy;
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche “Mario Negri”—IRCCS, 20156 Milano, Italy;
| | - Sara Wellens
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Maxime Culot
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Fabien Gosselet
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-01-476-0253 (L.M.L. & M.N.)
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126
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Istanbullu H, Bayraktar G, Akbaba H, Cavus I, Coban G, Debelec Butuner B, Kilimcioglu AA, Ozbilgin A, Alptuzun V, Erciyas E. Design, synthesis, and in vitro biological evaluation of novel thiazolopyrimidine derivatives as antileishmanial compounds. Arch Pharm (Weinheim) 2020; 353:e1900325. [DOI: 10.1002/ardp.201900325] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/21/2020] [Accepted: 05/11/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Huseyin Istanbullu
- Department of Pharmaceutical Chemistry, Faculty of PharmacyIzmir Katip Celebi University Cigli Izmir Turkey
| | - Gulsah Bayraktar
- Department of Pharmaceutical Chemistry, Faculty of PharmacyEge University Bornova Izmir Turkey
| | - Hasan Akbaba
- Department of Pharmaceutical Biotechnology, Faculty of PharmacyEge University Bornova Izmir Turkey
| | - Ibrahim Cavus
- Department of ParasitologyManisa Celal Bayar University Manisa Turkey
| | - Gunes Coban
- Department of Pharmaceutical Chemistry, Faculty of PharmacyEge University Bornova Izmir Turkey
| | - Bilge Debelec Butuner
- Department of Pharmaceutical Biotechnology, Faculty of PharmacyEge University Bornova Izmir Turkey
| | | | - Ahmet Ozbilgin
- Department of ParasitologyManisa Celal Bayar University Manisa Turkey
| | - Vildan Alptuzun
- Department of Pharmaceutical Chemistry, Faculty of PharmacyEge University Bornova Izmir Turkey
| | - Ercin Erciyas
- Department of Pharmaceutical Chemistry, Faculty of PharmacyEge University Bornova Izmir Turkey
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127
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Wilkinson RC, Rahman Pour R, Jamshidi S, Fülöp V, Bugg TDH. Extracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to tobacco salicylic acid binding protein 2. J Struct Biol 2020; 210:107496. [PMID: 32224091 DOI: 10.1016/j.jsb.2020.107496] [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: 11/24/2019] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 10/24/2022]
Abstract
An alpha/ beta hydrolase annotated as a putative salicylate esterase within the genome of a species of Paenibacillus previously identified from differential and selective growth on Kraft lignin was structurally and functionally characterised. Feruloyl esterases are key to the degradation of lignin in several bacterial species and although this activity was investigated, no such activity was observed. The crystal structure of the Paenibacillus esterase, here denoted as PnbE, was determined at 1.32 Å resolution, showing high similarity to Nicotiana tabacum salicylic acid binding protein 2 from the protein database. Structural similarities between these two structures across the core domains and key catalytic residues were observed, with superposition of catalytic residues giving an RMSD of 0.5 Å across equivalent Cα atoms. Conversely, the cap domains of PnbE and Nicotiana tabacum SABP2 showed greater divergence with decreased flexibility in the PnbE cap structure. Activity of PnbE as a putative methyl salicylate esterase was supported with binding studies showing affinity for salicylic acid and functional studies showing methyl salicylate esterase activity. We hypothesise that this activity could enrich Paenibacillus sp. within the rhizosphere by increasing salicylic acid concentrations within the soil.
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Affiliation(s)
| | | | - Shirin Jamshidi
- School of Cancer and Pharmaceutical Sciences, King's College London, SE1 9NH, UK
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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128
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Li Y, Gao Y, Holloway MK, Wang R. Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. J Chem Inf Model 2020; 60:4359-4375. [DOI: 10.1021/acs.jcim.9b00619] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People’s Republic of China
| | - Yingduo Gao
- Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
- Merck Research Laboratories, 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | | | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People’s Republic of China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- Shanxi Key Laboratory of Innovative Drugs for the Treatment of Serious Diseases Basing on Chronic Inflammation, College of Traditional Chinese Medicines, Shanxi University of Chinese Medicine, Taiyuan, Shanxi 030619, People’s Republic of China
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129
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Wang K, Lyu N, Diao H, Jin S, Zeng T, Zhou Y, Wu R. GM-DockZn: a geometry matching-based docking algorithm for zinc proteins. Bioinformatics 2020; 36:4004-4011. [DOI: 10.1093/bioinformatics/btaa292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/06/2020] [Accepted: 04/27/2020] [Indexed: 12/23/2022] Open
Abstract
Abstract
Motivation
Molecular docking is a widely used technique for large-scale virtual screening of the interactions between small-molecule ligands and their target proteins. However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing docking methods developed specifically for zinc proteins, GM-DockZn samples ligand conformations directly using a geometric grid around the ideal zinc-coordination positions of seven discovered coordination motifs, which were found from the survey of known zinc proteins complexed with a single ligand.
Results
GM-DockZn has the best performance in sampling near-native poses with correct coordination atoms and numbers within the top 50 and top 10 predictions when compared to several state-of-the-art techniques. This is true not only for a non-redundant dataset of zinc proteins but also for a homolog set of different ligand and zinc-coordination systems for the same zinc proteins. Similar superior performance of GM-DockZn for near-native-pose sampling was also observed for docking to apo-structures and cross-docking between different ligand complex structures of the same protein. The highest success rate for sampling nearest near-native poses within top 5 and top 1 was achieved by combining GM-DockZn for conformational sampling with GOLD for ranking. The proposed geometry-based sampling technique will be useful for ligand docking to other metalloproteins.
Availability and implementation
GM-DockZn is freely available at www.qmclab.com/ for academic users.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kai Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006
- School of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510000
| | - Nan Lyu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006
| | - Hongjuan Diao
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006
| | - Shujuan Jin
- Peking University Shenzhen Graduate School, Shenzhen 518055
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Tao Zeng
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006
| | - Yaoqi Zhou
- Peking University Shenzhen Graduate School, Shenzhen 518055
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD 4222, Australia
| | - Ruibo Wu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD 4222, Australia
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130
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New acrylamide-sulfisoxazole conjugates as dihydropteroate synthase inhibitors. Bioorg Med Chem 2020; 28:115444. [DOI: 10.1016/j.bmc.2020.115444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022]
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131
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Gupta D, Singh A, Somvanshi P, Singh A, Khan AU. Structure-Based Screening of Non-β-Lactam Inhibitors against Class D β-Lactamases: An Approach of Docking and Molecular Dynamics. ACS OMEGA 2020; 5:9356-9365. [PMID: 32363287 PMCID: PMC7191842 DOI: 10.1021/acsomega.0c00356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
The manifestation of class D β-lactamases in the community raises significant concern as they can hydrolyze carbapenem antibiotics. Hence, it is exceptionally alluring to design novel inhibitors. Structure-based virtual screening using docking programs and molecular dynamics simulations was employed to identify two novel non-β-lactam compounds that possess the ability to block different OXA variants. Furthermore, the presence of a nonpolar aliphatic amino acid, valine, near the active site serine, was identified in all OXA variants that can be accounted to block the catalytic activity of OXA enzymes.
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Affiliation(s)
- Divya Gupta
- Interdisciplinary
Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India
- Department of Life Sciences, Uttarakhand
Technical University, Dehradun 248007 Uttarakhand, India
| | - Aditi Singh
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi 110070, India
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, New Delhi 110070, India
| | - Ajeet Singh
- Department of Biotechnology, G. B. Pant Engineering College, Pauri 246194, India
| | - Asad U. Khan
- Interdisciplinary
Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia
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132
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Sciortino G, Sánchez-Aparicio JE, Rodríguez-Guerra Pedregal J, Garribba E, Maréchal JD. Computational insight into the interaction of oxaliplatin with insulin. Metallomics 2020; 11:765-773. [PMID: 30724953 DOI: 10.1039/c8mt00341f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In an organism, cisplatin and its derivatives are known to interact with proteins besides their principal DNA target. These off-target interactions have major therapeutic consequences including undesired side effects, loss of bioavailability and emergence of resistance. Insulin is one of the prototypical protein targets of platinum drugs as it has been seen to be involved in bioavailability reduction and might also determine resistance in certain cancer lines. However, despite the interest in understanding the nature of the oxaliplatin-insulin adducts, no 3D models have been achieved so far. In this study, we apply our recent computational multiscale protocol optimized for bioinorganic interactions to provide structural insights into these systems. To do so, the initial structures are predicted by blind protein-metalloligand docking calculations optimized to account for a metal-containing species, and then refined using a Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) integrated protocol. The results are consistent with experimental information obtained from fragment analysis, and also provide novel structural information like conformational changes occurring upon binding and potential effects on the biological functions of the protein. This study opens an avenue towards applying similar strategies to a wide ensemble of metallodrug-protein/peptide systems for which no structural data are available.
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Affiliation(s)
- Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain.
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133
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Duan G, Ji C, Zhang JZH. Developing an effective polarizable bond method for small molecules with application to optimized molecular docking. RSC Adv 2020; 10:15530-15540. [PMID: 35495446 PMCID: PMC9052371 DOI: 10.1039/d0ra01483d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Electrostatic interaction plays an essential role in protein-ligand binding. Due to the polarization effect, electrostatic interactions are largely impacted by their local environments. However, traditional force fields use fixed point charge-charge interactions to describe electrostatic interactions but is unable to include the polarization effect. The lack of the polarization effect in the force field representation can result in substantial error in biomolecular studies, such as molecular dynamics and molecular docking. Docking programs usually employ traditional force fields to estimate the binding energy between a ligand and a protein for pose selection or scoring. The intermolecular interaction energy mainly consists of van der Waals and electrostatic interaction in the force field representation. In the current study, we developed an Effective Polarizable Bond (EPB) method for small organic molecules and applied this EPB method to optimize protein-ligand docking in computational tests for a variety of protein-ligand systems. We tested the method on a set of 38 cocrystallized structures taken from the Protein Data Bank (PDB) and found that the maximum error was reduced from 7.98 Å to 2.03 Å when using EPB Dock, providing strong evidence that the use of EPB charges is important. We found that our optimized docking approach with EPB charges could improve the docking performance, sometimes dramatically, and the maximum error was reduced from 12.88 Å to 1.57 Å in Optimized Docking (in the case of 1fqx). The average RMSD decreased from 2.83 Å to 1.85 Å. Further investigations showed that the use of the EBP method could enhance intermolecular hydrogen bonding, which is a major contributing factor to improved docking performance. Developed tools for the calculation of the polarized ligand charge from a protein-ligand complex structure with the EPB method are freely available on GitHub (https://github.com/Xundrug/EPB).
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Affiliation(s)
- Guanfu Duan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
- Department of Chemistry, New York University NY NY 10003 USA
- Collaborative Innovation Center of Extreme Optics, Shanxi University Taiyuan Shanxi 030006 China
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134
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Tao H, Zhang Y, Huang SY. Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. J Chem Inf Model 2020; 60:2377-2387. [PMID: 32267149 DOI: 10.1021/acs.jcim.0c00058] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein-peptide docking, which predicts the complex structure between a protein and a peptide, is a valuable computational tool in peptide therapeutics development and the mechanistic investigation of peptides involved in cellular processes. Although current peptide docking approaches are often able to sample near-native peptide binding modes, correctly identifying those near-native modes from decoys is still challenging because of the extremely high complexity of the peptide binding energy landscape. In this study, we have developed an efficient postdocking rescoring protocol using a combined scoring function of knowledge-based ITScorePP potentials and physics-based MM-GBSA energies. Tested on five benchmark/docking test sets, our postdocking strategy showed an overall significantly better performance in binding mode prediction and score-rmsd correlation than original docking approaches. Specifically, our postdocking protocol outperformed original docking approaches with success rates of 15.8 versus 10.5% for pepATTRACT on the Global_57 benchmark, 5.3 versus 5.3% for CABS-dock on the Global_57 benchmark, 17.0 versus 11.3% for FlexPepDock on the LEADS-PEP data set, 40.3 versus 33.9% for HPEPDOCK on the Local_62 benchmark, and 64.2 versus 52.8% for HPEPDOCK on the LEADS-PEP data set when the top prediction was considered. These results demonstrated the efficacy and robustness of our postdocking protocol.
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Affiliation(s)
- Huanyu Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Yanjun Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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135
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Talarico C, Gervasoni S, Manelfi C, Pedretti A, Vistoli G, Beccari AR. Combining Molecular Dynamics and Docking Simulations to Develop Targeted Protocols for Performing Optimized Virtual Screening Campaigns on The hTRPM8 Channel. Int J Mol Sci 2020; 21:E2265. [PMID: 32218173 PMCID: PMC7177470 DOI: 10.3390/ijms21072265] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND There is an increasing interest in TRPM8 ligands of medicinal interest, the rational design of which can be nowadays supported by structure-based in silico studies based on the recently resolved TRPM8 structures. Methods: The study involves the generation of a reliable hTRPM8 homology model, the reliability of which was assessed by a 1.0 μs MD simulation which was also used to generate multiple receptor conformations for the following structure-based virtual screening (VS) campaigns; docking simulations utilized different programs and involved all monomers of the selected frames; the so computed docking scores were combined by consensus approaches based on the EFO algorithm. Results: The obtained models revealed very satisfactory performances; LiGen™ provided the best results among the tested docking programs; the combination of docking results from the four monomers elicited a markedly beneficial effect on the computed consensus models. Conclusions: The generated hTRPM8 model appears to be amenable for successful structure-based VS studies; cross-talk modulating effects between interacting monomers on the binding sites can be accounted for by combining docking simulations as performed on all the monomers; this strategy can have general applicability for docking simulations involving quaternary protein structures with multiple identical binding pockets.
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Affiliation(s)
- Carmine Talarico
- Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy; (C.T.); (C.M.)
| | - Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (A.P.); (G.V.)
| | - Candida Manelfi
- Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy; (C.T.); (C.M.)
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (A.P.); (G.V.)
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milano, Italy; (S.G.); (A.P.); (G.V.)
| | - Andrea R. Beccari
- Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy; (C.T.); (C.M.)
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136
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Wang H, Reinecke BA, Zhang Y. Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators. J Comput Aided Mol Des 2020; 34:879-895. [PMID: 32193867 DOI: 10.1007/s10822-020-00309-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 03/14/2020] [Indexed: 11/27/2022]
Abstract
Targeting the mu opioid receptor (MOR) by applying orthosteric ligands is the most frequently employed method to treat opioid use disorder (OUD). Unfortunately, most of MOR orthosteric ligands produce severe side effects, mainly due to their low selectivity over other opioid receptors. In contrast, some G protein-coupled receptor allosteric modulators have been reported to exhibit high subtype selectivity and can effectively modulate the potency and/or efficacy of orthosteric ligands. Recently, NAQ and its analog NCQ were identified as novel MOR bitopic modulators. Interestingly, NAQ and NCQ were similar in structure but exhibited different efficacy profiles to the MOR. NAQ exhibited an antagonism activity to the MOR while NCQ showed a partial agonism activity to the MOR. In the present study, molecular modeling methods were applied to explore the putative molecular mechanisms of their different functional profiles to the MOR. When NAQ binding with the inactive MOR, the 'address' portion of NAQ interacted with the MOR allosteric site but showed no significant allosteric modulation of the efficacy of the 'message' portion of NAQ. However, when NCQ binding with the inactive and active MOR, the 'address' portion of NCQ seemed to be able to positively modulate the efficacy of the 'message' portion of NCQ at varying levels. Evidentially, the substituents at the 1'- and 4'-positions of the isoquinoline ring of NCQ seemed to play a critical role in the modulatory function of the 'address' portion of NCQ. These findings will be invaluable to develop our next generation of MOR bitopic modulators with high affinity and subtype selectivity to potentially treat OUD.
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Affiliation(s)
- Huiqun Wang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA
| | - Bethany A Reinecke
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA.
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137
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Ahmad F, Azam SS. Role of ring positioning and preferential occupation of ligand obtained through molecular dynamics simulation of peptidoglycan associated lipoprotein (Pal). J Mol Graph Model 2020; 98:107585. [PMID: 32304985 DOI: 10.1016/j.jmgm.2020.107585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
Peptidoglycan associated lipoprotein (Pal) of Burkholderia cepacia is a highly attractive target as it is essential and conserved across strains of the pathogen and involved significantly in pathogenesis and survival. Herein, we used this target in virtual screening of small drug molecules library with an objective to screen the most appropriate antagonist for (Pal) to block its biological function. Results yielded a pyrimidine with imidazole group of compound "(R)-2-(1-(2, 6-dioxo-1, 2, 3, 6-tetrahydropyrimidine-4-carbonyl) piperidin-3-yl)-5-methlimidazol-3-ium-1-ide" showing the highest affinity for the active pocket of the protein and posed as such that the pyrimidine-4-carbonyl and piperidin-3-yl ring of the molecule is docked deep inside the pocket keeping the (R)-2-(piperidin-3-yl)imidazole-3-ium-1-ide posed outside this cavity. Molecular dynamics (MD) simulations illustrated stable binding of the compound at the docked site throughout the course of 600 ns (ns) with no conformational changes observed in the receptor macromolecule. Higher conformational stability was inferred for the system with mean RMSD of 1.1 Å supported with residual flexibility with mean value of 0.7 Å. Radial distribution function (RDF) showed the profound involvement of Arg56, Asp20 and Asp54 from protein active pocket in hydrogen bonding at the beginning and towards the end of simulation. The binding energy MMPB/GBSA and WaterSwap analyses showed an earnest contract on the affinity of inhibitor in response to hotspot residues of the active pocket. The role of stable positioning of rings inside the cavity is established through simulation, while a relevant comparative analysis indicates the compound as biologically active and potent candidate for therapeutic applications.
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Affiliation(s)
- Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan.
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, Pakistan.
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138
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Taira J, Umei T, Inoue K, Kitamura M, Berenger F, Sacchettini JC, Sakamoto H, Aoki S. Improvement of the novel inhibitor for Mycobacterium enoyl-acyl carrier protein reductase (InhA): a structure-activity relationship study of KES4 assisted by in silico structure-based drug screening. J Antibiot (Tokyo) 2020; 73:372-381. [PMID: 32152525 DOI: 10.1038/s41429-020-0293-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/09/2020] [Accepted: 02/10/2020] [Indexed: 11/09/2022]
Abstract
InhA or enoyl-acyl carrier protein reductase of Mycobacterium tuberculosis (mtInhA), which controls mycobacterial cell wall construction, has been targeted in the development of antituberculosis drugs. Previously, our in silico structure-based drug screening study identified a novel class of compounds (designated KES4), which is capable of inhibiting the enzymatic activity of mtInhA, as well as mycobacterial growth. The compounds are composed of four ring structures (A-D), and the MD simulation predicted specific interactions with mtInhA of the D-ring and methylene group between the B-ring and C-ring; however, there is still room for improvement in the A-ring structure. In this study, a structure-activity relationship study of the A-ring was attempted with the assistance of in silico docking simulations. In brief, the virtual chemical library of A-ring-modified KES4 was constructed and subjected to in silico docking simulation against mtInhA using the GOLD program. Among the selected candidates, we achieved synthesis of seven compounds, and the bioactivities (effects on InhA activity and mycobacterial growth and cytotoxicity) of the synthesized molecules were evaluated. Among the compounds tested, two candidates (compounds 3d and 3f) exhibited superior properties as mtInhA-targeted anti-infectives for mycobacteria than the lead compound KES4.
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Affiliation(s)
- Junichi Taira
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Tomohiro Umei
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Keitaro Inoue
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Mitsuru Kitamura
- Department of Applied Chemistry, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, 804-8550, Japan
| | - Francois Berenger
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - James C Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Hiroshi Sakamoto
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan
| | - Shunsuke Aoki
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, 820-8502, Japan.
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139
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Carvalho Bertozo L, Fernandes AJFC, Yoguim MI, Bolean M, Ciancaglini P, Ximenes VF. Entropy‐driven binding of octyl gallate in albumin: Failure in the application of temperature effect to distinguish dynamic and static fluorescence quenching. J Mol Recognit 2020; 33:e2840. [DOI: 10.1002/jmr.2840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/25/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Luiza Carvalho Bertozo
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
| | - Ana J. F. C. Fernandes
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
| | - Maurício I. Yoguim
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
| | - Maytê Bolean
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters at Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Pietro Ciancaglini
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters at Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Valdecir F. Ximenes
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
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140
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Abstract
Recently, machine learning (ML) has established itself in various worldwide benchmarking competitions in computational biology, including Critical Assessment of Structure Prediction (CASP) and Drug Design Data Resource (D3R) Grand Challenges. However, the intricate structural complexity and high ML dimensionality of biomolecular datasets obstruct the efficient application of ML algorithms in the field. In addition to data and algorithm, an efficient ML machinery for biomolecular predictions must include structural representation as an indispensable component. Mathematical representations that simplify the biomolecular structural complexity and reduce ML dimensionality have emerged as a prime winner in D3R Grand Challenges. This review is devoted to the recent advances in developing low-dimensional and scalable mathematical representations of biomolecules in our laboratory. We discuss three classes of mathematical approaches, including algebraic topology, differential geometry, and graph theory. We elucidate how the physical and biological challenges have guided the evolution and development of these mathematical apparatuses for massive and diverse biomolecular data. We focus the performance analysis on protein-ligand binding predictions in this review although these methods have had tremendous success in many other applications, such as protein classification, virtual screening, and the predictions of solubility, solvation free energies, toxicity, partition coefficients, protein folding stability changes upon mutation, etc.
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Affiliation(s)
- Duc Duy Nguyen
- Department of Mathematics, Michigan State University, MI 48824, USA.
| | - Zixuan Cang
- Department of Mathematics, Michigan State University, MI 48824, USA.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, MI 48824, USA. and Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA and Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
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141
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Lalut J, Payan H, Davis A, Lecoutey C, Legay R, Sopkova-de Oliveira Santos J, Claeysen S, Dallemagne P, Rochais C. Rational design of novel benzisoxazole derivatives with acetylcholinesterase inhibitory and serotoninergic 5-HT 4 receptors activities for the treatment of Alzheimer's disease. Sci Rep 2020; 10:3014. [PMID: 32080261 PMCID: PMC7033111 DOI: 10.1038/s41598-020-59805-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 01/30/2020] [Indexed: 01/09/2023] Open
Abstract
A rigidification strategy was applied to the preclinical candidate donecopride, an acetylcholinesterase inhibitor possessing 5-HT4R agonist activity. Inspired by promising bioactive benzisoxazole compounds, we have conducted a pharmacomodulation study to generate a novel series of multitarget directed ligands. The chemical synthesis of the ligand was optimized and compounds were evaluated in vitro against each target and in cellulo. Structure-activity relationship was supported by docking analysis in human acetylcholinesterase binding site. Among the synthesized compounds, we have identified a novel hybrid 32a (3-[2-[1-(cyclohexylmethyl)-4-piperidyl]ethyl]-4-methoxy-1,2-benzoxazole) able to display nanomolar acetylcholinesterase inhibitory effects and nanomolar Ki for 5-HT4R.
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Affiliation(s)
- Julien Lalut
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | - Hugo Payan
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Audrey Davis
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | - Cédric Lecoutey
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | - Rémi Legay
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | | | | | - Patrick Dallemagne
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | - Christophe Rochais
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France.
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142
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Majewski M, Barril X. Structural Stability Predicts the Binding Mode of Protein–Ligand Complexes. J Chem Inf Model 2020; 60:1644-1651. [DOI: 10.1021/acs.jcim.9b01062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maciej Majewski
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, Barcelona 08028, Spain
| | - Xavier Barril
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain
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143
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Rehman A, Ullah R, Gupta D, Khan MH, Rehman L, Beg MA, Khan AU, Abidi S. Generation of oxidative stress and induction of apoptotic like events in curcumin and thymoquinone treated adult Fasciola gigantica worms. Exp Parasitol 2020; 209:107810. [DOI: 10.1016/j.exppara.2019.107810] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/28/2019] [Accepted: 11/30/2019] [Indexed: 12/12/2022]
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144
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Çoban G, Aydın Köse F. Synthesis, biological evaluations and molecular modelling studies of novel indolin-2-ones designing as FGFR inhibitors. Saudi Pharm J 2020; 27:952-967. [PMID: 31997902 PMCID: PMC6978637 DOI: 10.1016/j.jsps.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/10/2019] [Indexed: 11/25/2022] Open
Abstract
A series of novel 3,5-disubstituted indolin-2-ones were designed and synthesized as selective FGFR inhibitors. In the design process of 3,5-disubstituted indolin-2-ones for FGFRs, molecular docking studies were performed to generate and optimize novel compounds which have FGFR inhibitory potency, theoretically. In vitro enzyme inhibitory and selectivity profiles of the synthesized compounds, and their cytotoxicity against NIH-3T3 cells were evaluated. According to enzyme inhibition assay, compound A1 (FGFR1-4; IC50 = 19.82; 5.95; 1419; 37150 nM), compound A5 (FGFR1-4; IC50 = 1890; Nd; 6.50; 18590 nM) and compound A13 (FGFR1-4; IC50 = 6.99; 1022; 17090; 8993 nM) have displayed best inhibitory potency against FGFR2, FGFR3 and FGFR1, respectively. The studied compounds have displayed low affinity to FGFR4 in comparison with other isoforms. Molecular docking study data were used to determine the binding orientations of the synthesized compounds inside FGFRs in accordance with enzyme inhibition assay data. Molecular dynamics simulations and free energy calculations were performed to determine stability, binding modes and dynamics behaviors of compound A1, A5 and A13 inside FGFR-2, FGFR-3 and FGFR-1, respectively. The compounds bearing aromatic groups at the C5 position of indolin-2-one could be lead compounds for the development of more effective and selective FGFR1-3 inhibitors.
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Affiliation(s)
- Güneş Çoban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, 35040 Bornova, Izmir, Turkey
| | - Fadime Aydın Köse
- Department of Biochemistry, Faculty of Pharmacy, Ege University, 35040 Bornova, Izmir, Turkey
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145
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Zangerl-Plessl EM, Berger M, Drescher M, Chen Y, Wu W, Maulide N, Sanguinetti M, Stary-Weinzinger A. Toward a Structural View of hERG Activation by the Small-Molecule Activator ICA-105574. J Chem Inf Model 2020; 60:360-371. [PMID: 31877041 DOI: 10.1021/acs.jcim.9b00737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Outward current conducted by human ether-à-go-go-related gene type 1 (hERG1) K+ channels is important for action potential repolarization in the human ventricle. Rapid, voltage-dependent inactivation greatly reduces outward currents conducted by hERG1 channels and involves conformational changes in the ion selectivity filter (SF). Recently, compounds have been found that activate hERG1 channel function by modulating gating mechanisms such as reducing inactivation. Such activating compounds could represent a novel approach to prevent arrhythmias associated with prolonged ventricular repolarization associated with inherited or acquired long QT syndrome. ICA-105574 (ICA), a 3-nitro-n-(4-phenoxyphenyl) benzamide derivative activates hERG1 by strongly attenuating pore-type inactivation. We previously mapped the putative binding site for ICA to a hydrophobic pocket located between two adjacent subunits. Here, we used the recently reported cryoelectron microscopy structures of hERG1 to elucidate the structural mechanisms by which ICA influences the stability of the SF. By combining molecular dynamics simulations, voltage-clamp electrophysiology, and the synthesis of novel ICA derivatives, we provide atomistic insights into SF dynamics and propose a structural link between the SF and S6 segments. Further, our study highlights the importance of the nitro moiety, at the meta position of the benzamide ring, for the activity of ICA and reveals that the (bio)isosteric substitution of this side chain can switch the activity to weak inhibitors. Our findings indicate that ICA increases the stability of the SF to attenuate channel inactivation, and this action requires a fine-tuned compound geometry.
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Affiliation(s)
- Eva-Maria Zangerl-Plessl
- Department of Pharmacology and Toxicology , University of Vienna , Althanstrasse 14 , Wien , Vienna 1090 , Austria
| | - Martin Berger
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Martina Drescher
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Yong Chen
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Wei Wu
- Nora Eccles Harrison Cardiovascular Research and Training Institute and Division of Cardiovascular Medicine, Department of Internal Medicine , University of Utah , Salt Lake City , Utah 84132-340 , United States
| | - Nuno Maulide
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Michael Sanguinetti
- Nora Eccles Harrison Cardiovascular Research and Training Institute and Division of Cardiovascular Medicine, Department of Internal Medicine , University of Utah , Salt Lake City , Utah 84132-340 , United States
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology , University of Vienna , Althanstrasse 14 , Wien , Vienna 1090 , Austria
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146
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Cardoso FF, Gomes AAS, Dreyer TR, Cavalcante WLG, Dal Pai M, Gallacci M, Fontes MRM. Neutralization of a bothropic PLA 2-like protein by caftaric acid, a novel potent inhibitor of ophidian myotoxicity. Biochimie 2020; 170:163-172. [PMID: 31978419 DOI: 10.1016/j.biochi.2020.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/19/2020] [Indexed: 11/18/2022]
Abstract
Envenoming by snakebite is an important global health issue that has received little attention, leading the World Health Organization to naming it as neglected tropical disease. Several snakebites present serious local symptoms manifested on victims that may not be efficiently neutralized by serum therapy. Phospholipase A2-like (PLA2-like) toxins are present in Viperidae venoms and are responsible for local myotoxic activity. Herein, we investigated the association between BthTX-I toxin and caftaric acid (CFT), a molecule present in plants. CFT neutralized neuromuscular blocking and muscle-damaging activities promoted by BthTX-I. Calorimetric and light-scattering assays demonstrated that CFT inhibitor interacted with dimeric BthTX-I. Bioinformatics simulations indicated that CFT inhibitor binds to the toxin's hydrophobic channel (HCh). According to the current myotoxic mechanism, three different regions of PLA2-like toxins have specific tasks: protein allosteric activation (HCh), membrane dockage (MDoS), and membrane rupture (MDiS). We propose CFT inhibitor interferes with the allosteric activation, which is related to the conformation change leading to the exposure/alignment of MDoS/MDiS region. This is the first report of a PLA2-like toxin fully inhibited by a compound that interacts only with its HCh region. Thus, CFT is a novel candidate to complement serum therapy and improve the treatment of snakebite.
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Affiliation(s)
- Fábio F Cardoso
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Antoniel A S Gomes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Thiago R Dreyer
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Walter L G Cavalcante
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Maeli Dal Pai
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Márcia Gallacci
- Departamento de Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil.
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147
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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148
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Lima HGD, Santos FO, Santos ACV, Silva GDD, Santos RJD, Carneiro KDO, Reis IMA, Estrela IDO, Freitas HFD, Bahiense TC, Pita SSDR, Uzeda RS, Branco A, Costa SL, Batatinha MJM, Botura MB. Anti-tick effect and cholinesterase inhibition caused by Prosopis juliflora alkaloids: in vitro and in silico studies. REVISTA BRASILEIRA DE PARASITOLOGIA VETERINARIA 2020; 29:e019819. [DOI: 10.1590/s1984-29612020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/30/2020] [Indexed: 01/23/2023]
Abstract
Abstract We investigated the in vitro acaricide activity of the methanolic extract (ME) and alkaloid-rich fraction (AF) of Prosopis juliflora on Rhipicephalus microplus and correlated this effect with acetylcholinesterase (AChE) inhibition. The acaricide activity was evaluated using adult and larval immersion tests. Also, we studied the possible interaction mechanism of the major alkaloids present in this fraction via molecular docking at the active site of R. microplus AChE1 (RmAChE1). Higher reproductive inhibitory activity of the AF was recorded, with effective concentration (EC50) four times lower than that of the ME (31.6 versus 121 mg/mL). The AF caused mortality of tick larvae, with lethal concentration 50% (LC50) of 13.8 mg/mL. Both ME and AF were seen to have anticholinesterase activity on AChE of R. microplus larvae, while AF was more active with half-maximal inhibitory concentration (IC50) of 0.041 mg/mL. The LC-MS/MS analyses on the AF led to identification of three alkaloids: prosopine (1), juliprosinine (2) and juliprosopine (3). The molecular docking studies revealed that these alkaloids had interactions at the active site of the RmAChE1, mainly relating to hydrogen bonds and cation-pi interactions. We concluded that the alkaloids of P. juliflora showed acaricide activity on R. microplus and acted through an anticholinesterase mechanism.
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149
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Ibrahim TM, Ernst C, Lange A, Hennig S, Boeckler FM. Small-Molecule Intervention At The Dimerization Interface Of Survivin By Novel Rigidized Scaffolds. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:4247-4263. [PMID: 31908412 PMCID: PMC6927794 DOI: 10.2147/dddt.s224561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/12/2019] [Indexed: 11/24/2022]
Abstract
Introduction Survivin is a nodal protein involved in several cellular pathways. It is a member of the IAP family and an integral component of the chromosomal passenger complex, where it binds to borealin and INCENP through its dimerization interface. By targeting survivin with a small molecule at its dimerization interface, inhibition of the proliferation of cancer cells has been suggested. With Abbott 8, a small-molecule dimerization inhibitor has been recently reported. The structure–activity relationship of this series of inhibitors implied that the middle pyridin-2(1H)-one ring did not tolerate modifications of any kind. Methods Based on the synthetic strategy of Abbott 8 using multicomponent reactions, we synthesized a series of small molecules bearing a novel rigidized core scaffold. This rigidization strategy was accomplished by integrating the pyridin-2(1H)-one and its 6-phenyl substituent into a tricyclic structure, linking position 5 of pyridin-2(1H)-one to the phenyl substituent by rings of different sizes. The new scaffolds were designed based on in silico molecular dynamics of survivin. Results Binding of these rigidized scaffolds to the recombinant L54M mutant of survivin was evaluated, revealing affinities in the low micromolar range. Conclusion This easily accessible, new class of survivin-dimerization modulators is an interesting starting point for further lead optimization.
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Affiliation(s)
- Tamer M Ibrahim
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tübingen, Tübingen, Germany.,Pharmaceutical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Christoph Ernst
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas Lange
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Susanne Hennig
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tübingen, Tübingen, Germany
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150
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Nafie MS, Tantawy MA, Elmgeed GA. Screening of different drug design tools to predict the mode of action of steroidal derivatives as anti-cancer agents. Steroids 2019; 152:108485. [PMID: 31491446 DOI: 10.1016/j.steroids.2019.108485] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/18/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022]
Abstract
There is a pressing need to discover and develop novel drugs against cancer. With the new era of bioinformatics, which integrates different aspects, drug development has been tremendously improved. Recently, extensive research was directed towards the rational modification of steroid molecules against different disease especially cancer. Moreover, heterocyclic steroid derivatives have shown a lot of different biological activities such as antimicrobial, anti-inflammatory, and anti-cancer activities. Molecular docking methods can be used to explore how the steroid derivatives conformations can adopt within the binding sites of specific macromolecular targets involved in cancer progression. We conducted this study to investigate the accuracy of different molecular docking calculations using different steroidal molecular targets, and to define the most accurate one to study the mode of action of steroid derivatives as potential anti-cancer drugs. Our results revealed that the Dock6, PLANTS, AutoDock, GLIDE (SP and XP), and GOLD (ASP, Chemscore, and PLP) software were able to maintain the binding mode of the co-crystallized ligands inside their proteins by achieving RMSD values lower than two. Moreover, molecular docking study revealed that compound 4, and 5 are promising steroidal derivatives as anti-cancer drugs. Further on, the cytotoxic activity of the selected steroidal derivatives were tested against leukemia cell line using MTT assay. The results revealed that compound 4, and 5 were potential cytotoxic agents against THP-1 cells (IC50s were 44.67 µM, and 46.77 µM, respectively), these results are in agreement with the molecular docking study.
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Affiliation(s)
- Mohamed S Nafie
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Mohamed A Tantawy
- Hormones Department, Medical Research Division, National Research Centre, Cairo, Egypt; Stem Cells Lab, Center of Excellence for Advanced Sciences, National Research Centre, Dokki, Cairo, Egypt.
| | - Gamal A Elmgeed
- Hormones Department, Medical Research Division, National Research Centre, Cairo, Egypt
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