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Chidambaram K. Identification of BACE-1 Inhibitors against Alzheimer’s Disease through E-Pharmacophore-Based Virtual Screening and Molecular Dynamics Simulation Studies: An Insilco Approach. Life (Basel) 2023; 13:life13040952. [PMID: 37109481 PMCID: PMC10142975 DOI: 10.3390/life13040952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/01/2023] [Accepted: 03/31/2023] [Indexed: 04/09/2023] Open
Abstract
Alzheimer is a severe memory and cognitive impairment neurodegenerative disease that is the most common cause of dementia worldwide and characterized by the pathological accumulation of tau protein and amyloid-beta peptides. In this study, we have developed E-pharmacophore modeling to screen the eMolecules database with the help of a reported co-crystal structure bound with Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE-1). Flumemetamol, florbetaben, and florbetapir are currently approved drugs for use in the clinical diagnosis of Alzheimer’s disease. Despite the benefits of commercially approved drugs, there is still a need for novel diagnostic agents with enhanced physicochemical and pharmacokinetic properties compared to those currently used in clinical practice and research. In the E-pharmacophore modeling results, it is revealed that two aromatic rings (R19, R20), one donor (D12), and one acceptor (A8) are obtained, and also that similar pharmacophoric features of compounds are identified from pharmacophore-based virtual screening. The identified screened hits were filtered for further analyses using structure-based virtual screening and MM/GBSA. From the analyses, top hits such as ZINC39592220 and en1003sfl.46293 are selected based on their top docking scores (−8.182 and −7.184 Kcal/mol, respectively) and binding free energy (−58.803 and −56.951 Kcal/mol, respectively). Furthermore, a molecular dynamics simulation and MMPBSA study were performed, which revealed admirable stability and good binding free energy throughout the simulation period. Moreover, Qikprop results revealed that the selected, screened hits have good drug-likeness and pharmacokinetic properties. The screened hits ZINC39592220 and en1003sfl.46293 could be used to develop drug molecules against Alzheimer’s disease.
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Affiliation(s)
- Kumarappan Chidambaram
- Department of Pharmacology and Toxicology, College of Pharmacy, Al-Qara Campus, King Khalid University, Asir Province, Abha 61421, Saudi Arabia
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2
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Sellami A, Réau M, Montes M, Lagarde N. Review of in silico studies dedicated to the nuclear receptor family: Therapeutic prospects and toxicological concerns. Front Endocrinol (Lausanne) 2022; 13:986016. [PMID: 36176461 PMCID: PMC9513233 DOI: 10.3389/fendo.2022.986016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Being in the center of both therapeutic and toxicological concerns, NRs are widely studied for drug discovery application but also to unravel the potential toxicity of environmental compounds such as pesticides, cosmetics or additives. High throughput screening campaigns (HTS) are largely used to detect compounds able to interact with this protein family for both therapeutic and toxicological purposes. These methods lead to a large amount of data requiring the use of computational approaches for a robust and correct analysis and interpretation. The output data can be used to build predictive models to forecast the behavior of new chemicals based on their in vitro activities. This atrticle is a review of the studies published in the last decade and dedicated to NR ligands in silico prediction for both therapeutic and toxicological purposes. Over 100 articles concerning 14 NR subfamilies were carefully read and analyzed in order to retrieve the most commonly used computational methods to develop predictive models, to retrieve the databases deployed in the model building process and to pinpoint some of the limitations they faced.
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Mubassir MHM, Naser MA, Abdul-Wahab MF, Jawad T, Alvy RI, Hamdan S. Comprehensive in silico modeling of the rice plant PRR Xa21 and its interaction with RaxX21-sY and OsSERK2. RSC Adv 2020; 10:15800-15814. [PMID: 35493652 PMCID: PMC9052883 DOI: 10.1039/d0ra01396j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/15/2020] [Indexed: 12/19/2022] Open
Abstract
The first layer of defense that plants deploy to ward off a microbial invasion comes in the form of pattern-triggered immunity (PTI), which is initiated when the pattern-recognition receptors (PRRs) bind with the pathogen-associated molecular patterns (PAMPs) and co-receptor proteins, and transmit a defense signal. Although several plant PRRs have been discovered, very few of them have been fully characterized, and their functional parameters assessed. In this study, the 3D-model prediction of an entire plant PRR protein, Xa21, was done by implementing multiple in silico modeling techniques. Subsequently, the PAMP RaxX21-sY (sulphated RaxX21) and leucine-rich repeat (LRR) domain of the co-receptor OsSERK2 were docked with the LRR domain of Xa21. The docked complex of these three proteins formed a heterodimer that closely resembles the other crystallographic PTI complexes available. Molecular dynamics simulations and MM/PBSA calculations were applied for an in-depth analysis of the interactions between Xa21 LRR, RaxX21-sY, and OsSERK2 LRR. Arg230 and Arg185 from Xa21 LRR, Val2 and Lys15 from RaxX21-sY and Lys164 from OsSERK2 LRR were found to be the prominent residues which might contribute significantly in the formation of a heterodimer during the PTI process mediated by Xa21. Additionally, RaxX21-sY interacted much more favorably with Xa21 LRR in the presence of OsSERK2 LRR in the complex, which substantiates the necessity of the co-receptor in Xa21 mediated PTI to recognize the PAMP RaxX21-sY. However, the free energy binding calculation reveals the favorability of a heterodimer formation of PRR Xa21 and co-receptor OsSERK2 without the presence of PAMP RaxX21-sY, which validate the previous lab result.
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Affiliation(s)
- M H M Mubassir
- Department of Mathematics and Natural Sciences, BRAC University 66 Mohakhali Dhaka-1212 Bangladesh
| | - M Abu Naser
- Faculty Bioscience and Medical Engineering, Universiti Teknologi Malaysia 81310 Johor Bahru Johor Malaysia
| | - Mohd Firdaus Abdul-Wahab
- Faculty Bioscience and Medical Engineering, Universiti Teknologi Malaysia 81310 Johor Bahru Johor Malaysia
| | - Tanvir Jawad
- Department of Mathematics and Natural Sciences, BRAC University 66 Mohakhali Dhaka-1212 Bangladesh
| | - Raghib Ishraq Alvy
- Department of Mathematics and Natural Sciences, BRAC University 66 Mohakhali Dhaka-1212 Bangladesh
| | - Salehhuddin Hamdan
- Faculty Bioscience and Medical Engineering, Universiti Teknologi Malaysia 81310 Johor Bahru Johor Malaysia
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Slater O, Kontoyianni M. The compromise of virtual screening and its impact on drug discovery. Expert Opin Drug Discov 2019; 14:619-637. [PMID: 31025886 DOI: 10.1080/17460441.2019.1604677] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: Docking and structure-based virtual screening (VS) have been standard approaches in structure-based design for over two decades. However, our understanding of the limitations, potential, and strength of these techniques has enhanced, raising expectations. Areas covered: Based on a survey of reports in the past five years, we assess whether VS: (1) predicts binding poses in agreement with crystallographic data (when available); (2) is a superior screening tool, as often claimed; (3) is successful in identifying chemical scaffolds that can be starting points for subsequent lead optimization cycles. Data shows that knowledge of the target and its chemotypes in postprocessing lead to viable hits in early drug discovery endeavors. Expert opinion: VS is capable of accurate placements in the pocket for the most part, but does not consistently score screening collections accurately. What matters is capitalization on available resources to get closer to a viable lead or optimizable series. Integration of approaches, subjective hit selection guided by knowledge of the receptor or endogenous ligand, libraries driven by experimental guides, validation studies to identify the best docking/scoring that reproduces experimental findings, constraints regarding receptor-ligand interactions, thoroughly designed methodologies, and predefined cutoff scoring criteria strengthen VS's position in pharmaceutical research.
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Affiliation(s)
- Olivia Slater
- a Department of Pharmaceutical Sciences , Southern Illinois University Edwardsville , Edwardsville , IL , USA
| | - Maria Kontoyianni
- a Department of Pharmaceutical Sciences , Southern Illinois University Edwardsville , Edwardsville , IL , USA
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Di Leva FS, Di Marino D, Limongelli V. Structural Insight into the Binding Mode of FXR and GPBAR1 Modulators. Handb Exp Pharmacol 2019; 256:111-136. [PMID: 31161298 DOI: 10.1007/164_2019_234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this chapter we provide an exhaustive overview of the binding modes of bile acid (BA) and non-BA ligands to the nuclear farnesoid X receptor (FXR) and the G-protein bile acid receptor 1 (GPBAR1). These two receptors play a key role in many diseases related to lipid and glucose disorders, thus representing promising pharmacological targets. We pay particular attention to the chemical and structural features of the ligand-receptor interaction, providing guidelines to achieve ligands endowed with selective or dual activity towards the receptor and paving the way to future drug design studies.
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Affiliation(s)
| | - Daniele Di Marino
- Faculty of Biomedical Sciences, Institute of Computational Science, Center for Computational Medicine in Cardiology, Università della Svizzera italiana (USI), Lugano, Switzerland.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples "Federico II", Naples, Italy. .,Faculty of Biomedical Sciences, Institute of Computational Science, Center for Computational Medicine in Cardiology, Università della Svizzera italiana (USI), Lugano, Switzerland.
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6
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Giancristofaro A, Barbosa AJM, Ammazzalorso A, Amoia P, De Filippis B, Fantacuzzi M, Giampietro L, Maccallini C, Amoroso R. Discovery of new FXR agonists based on 6-ECDCA binding properties by virtual screening and molecular docking. MEDCHEMCOMM 2018; 9:1630-1638. [PMID: 30393515 PMCID: PMC6194413 DOI: 10.1039/c8md00272j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/28/2018] [Indexed: 01/03/2023]
Abstract
FXR is a member of the nuclear receptor superfamily, which regulates the expression of various genes involved in bile acid, lipid and glucose metabolism. Targeting FXR with small molecules has been exploited to treat lipid-related disorders and diseases such as cholestasis, gallstones and hepatic disorders. In this work, we expand the existing pool of known FXR agonists using a fast hit-to-lead structure-based pharmacophore and docking screening protocol. A set of 25 molecules was selected after screening a large database of commercial chemicals, and experimental tests were carried out to demonstrate their ability to activate FXR. Three novel FXR agonists are reported, namely, one full agonist, more efficient than the endogenous ligand chenodeoxycholic acid, and two partial agonists.
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Affiliation(s)
- Antonella Giancristofaro
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
| | - Arménio J M Barbosa
- Chemistry Department , Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Alessandra Ammazzalorso
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
| | - Pasquale Amoia
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
| | - Barbara De Filippis
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
| | - Marialuigia Fantacuzzi
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
| | - Letizia Giampietro
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
| | - Cristina Maccallini
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
| | - Rosa Amoroso
- Department of Pharmacy , University of Chieti "G. d'Annunzio" , via dei vestini 31 , 66100 Chieti , Italy .
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7
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Proschak E, Stark H, Merk D. Polypharmacology by Design: A Medicinal Chemist's Perspective on Multitargeting Compounds. J Med Chem 2018; 62:420-444. [PMID: 30035545 DOI: 10.1021/acs.jmedchem.8b00760] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multitargeting compounds comprising activity on more than a single biological target have gained remarkable relevance in drug discovery owing to the complexity of multifactorial diseases such as cancer, inflammation, or the metabolic syndrome. Polypharmacological drug profiles can produce additive or synergistic effects while reducing side effects and significantly contribute to the high therapeutic success of indispensable drugs such as aspirin. While their identification has long been the result of serendipity, medicinal chemistry now tends to design polypharmacology. Modern in vitro pharmacological methods and chemical probes allow a systematic search for rational target combinations and recent innovations in computational technologies, crystallography, or fragment-based design equip multitarget compound development with valuable tools. In this Perspective, we analyze the relevance of multiple ligands in drug discovery and the versatile toolbox to design polypharmacology. We conclude that despite some characteristic challenges remaining unresolved, designed polypharmacology holds enormous potential to secure future therapeutic innovation.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , Universitaetsstrasse 1 , D-40225 , Duesseldorf , Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany.,Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences , Swiss Federal Institute of Technology (ETH) Zürich , Vladimir-Prelog-Weg 4 , CH-8093 Zürich , Switzerland
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8
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Affiliation(s)
- Norbert Handler
- RD&C Research, Development & Consulting GmbH; Neuwaldegger Strasse 35/2/3 Vienna 1170 Austria
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9
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Sasaki T, Mita M, Ikari N, Kuboyama A, Hashimoto S, Kaneko T, Ishiguro M, Shimizu M, Inoue J, Sato R. Identification of key amino acid residues in the hTGR5-nomilin interaction and construction of its binding model. PLoS One 2017; 12:e0179226. [PMID: 28594916 PMCID: PMC5464637 DOI: 10.1371/journal.pone.0179226] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 05/25/2017] [Indexed: 12/12/2022] Open
Abstract
TGR5, a member of the G protein-coupled receptor (GPCR) family, is activated by bile acids. Because TGR5 promotes energy expenditure and improves glucose homeostasis, it is recognized as a key target in treating metabolic diseases. We previously showed that nomilin, a citrus limonoid, activates TGR5 and confers anti-obesity and anti-hyperglycemic effects in mice. Information on the TGR5–nomilin interaction regarding molecular structure, however, has not been reported. In the present study, we found that human TGR5 (hTGR5) shows higher nomilin responsiveness than does mouse TGR5 (mTGR5). Using mouse–human chimeric TGR5, we also found that three amino acid residues (Q77ECL1, R80ECL1, and Y893.29) are important in the hTGR5–nomilin interaction. Based on these results, an hTGR5–nomilin binding model was constructed using in silico docking simulation, demonstrating that four hydrophilic hydrogen-bonding interactions occur between nomilin and hTGR5. The binding mode of hTGR5–nomilin is vastly different from those of other TGR5 agonists previously reported, suggesting that TGR5 forms various binding patterns depending on the type of agonist. Our study promotes a better understanding of the structure of TGR5, and it may be useful in developing and screening new TGR5 agonists.
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Affiliation(s)
- Takashi Sasaki
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Moeko Mita
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Naho Ikari
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Ayane Kuboyama
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Shuzo Hashimoto
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Tatsuya Kaneko
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Masaji Ishiguro
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima, Akiha-ku, Niigata, Japan
| | - Makoto Shimizu
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Jun Inoue
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Ryuichiro Sato
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- Nutri-Life Science Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, Japan
- * E-mail:
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Krishna S, Shukla S, Lakra AD, Meeran SM, Siddiqi MI. Identification of potent inhibitors of DNA methyltransferase 1 (DNMT1) through a pharmacophore-based virtual screening approach. J Mol Graph Model 2017; 75:174-188. [PMID: 28582695 DOI: 10.1016/j.jmgm.2017.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation is an epigenetic change that results in the addition of a methyl group at the carbon-5 position of cytosine residues. DNA methyltransferase (DNMT) inhibitors can suppress tumour growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. Additionally, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects. In the present study, we have designed a workflow by integrating various ligand-based and structure-based approaches to discover new agents active against DNMT1. We have derived a pharmacophore model with the help of available DNMT1 inhibitors. Utilising this model, we performed the virtual screening of Maybridge chemical library and the identified hits were then subsequently filtered based on the Naïve Bayesian classification model. The molecules that have returned from this classification model were subjected to ensemble based docking. We have selected 10 molecules for the biological assay by inspecting the interactions portrayed by these molecules. Three out of the ten tested compounds have shown DNMT1 inhibitory activity. These compounds were also found to demonstrate potential inhibition of cellular proliferation in human breast cancer MDA-MB-231 cells. In the present study, we have utilized a multi-step virtual screening protocol to identify inhibitors of DNMT1, which offers a starting point to develop more potent DNMT1 inhibitors as anti-cancer agents.
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Affiliation(s)
- Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Samriddhi Shukla
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Amar Deep Lakra
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Syed Musthapa Meeran
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India.
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Sindhu T, Venkatesan T, Gracy GR, Jalali SK, Rai A. Exploring the resistance-developing mutations on Ryanodine receptor in diamondback moth and binding mechanism of its activators using computational study. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Lei B, Heng N, Dang X, Liu J, Yao X, Zhang C. Structure based in silico identification of potentially non-steroidal brassinosteroids mimics. MOLECULAR BIOSYSTEMS 2017; 13:1364-1369. [DOI: 10.1039/c7mb00214a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The identification of non-steroidal BRs-like molecules via structure-based pharmacophore virtual screening, molecular docking and bioassay.
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Affiliation(s)
- Beilei Lei
- Center of Bioinformatics
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
| | - Ningjuan Heng
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
| | - Xiaoxue Dang
- Center of Bioinformatics
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
| | - Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education
- Northwest A&F University
- Yangling
- China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Cunli Zhang
- College of Life Sciences
- Northwest A&F University
- Yangling
- China
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13
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Abstract
Molecular docking is a key tool in structural biology and computer-assisted drug design. Molecular docking is a method which predicts the preferred orientation of a ligand when bound in an active site to form a stable complex. It is the most common method used as a structure-based drug design. Here, the authors intend to discuss the various types of docking methods and their development and applications in modern drug discovery. The important basic theories such as sampling algorithm and scoring functions have been discussed briefly. The performances of the different available docking software have also been discussed. This chapter also includes some application examples of docking studies in modern drug discovery such as targeted drug delivery using carbon nanotubes, docking of nucleic acids to find the binding modes and a comparative study between high-throughput screening and structure-based virtual screening.
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14
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Hybrid Receptor-Bound/MM-GBSA-Per-residue Energy-Based Pharmacophore Modelling: Enhanced Approach for Identification of Selective LTA4H Inhibitors as Potential Anti-inflammatory Drugs. Cell Biochem Biophys 2016; 75:35-48. [PMID: 27914004 DOI: 10.1007/s12013-016-0772-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/15/2016] [Indexed: 10/20/2022]
Abstract
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and design of novel class of compounds that can selectively inhibit leukotriene B4 synthesis while sparing the aminopeptidase activity. Previous inhibitors block the dual activity of the enzyme. Recently, a small lead molecule inhibitor denoted as ARM1 has been identified to block the hydrolase activity of leukotriene A4 hydrolase whilst sparing the aminopeptidase activity. In this study, a hybrid receptor-bound/MM-GBSA-per-residue energy based pharmacophore modeling approach was implemented to identify potential selective hydrolase inhibitors of leukotriene A4 hydrolase. In this approach, active site residues that favorably contributed to the binding of the bound conformation of ARM1 were derived from MD ensembles and MM/GBSA thermodynamic calculations. These residues were then mapped to key pharmacophore features of ARM1. The generated pharmacophore model was used to search the ZINC database for 3D structures that match the pharmacophore. Five new compounds have been identified and proposed as potential epoxide hydrolase selective inhibitors of leukotriene A4 hydrolase. Molecular docking and MM/GBSA analyses revealed that, these top five lead-like compounds ZINC00142747, ZINC94260794, ZINC01382396, ZINC02508448, and ZINC53994447 showed better binding affinities to the hydrolase active site pocket compared to ARM1. Per-residue energy decomposition analysis revealed that amino acid residues Phe314, Tyr378, Pro382, Trp311, Val367, and Ala377 are key residues critical in the selective inhibition of these hits. Information highlighted in this study may guide the the design the next generation of novel and potent epoxide hydrolase selective inhibitors of leukotriene A4 hydrolase.
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15
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Yuan ZQ, Li KW. Role of farnesoid X receptor in cholestasis. J Dig Dis 2016; 17:501-509. [PMID: 27383832 DOI: 10.1111/1751-2980.12378] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/23/2016] [Accepted: 07/03/2016] [Indexed: 12/11/2022]
Abstract
The nuclear receptor farnesoid X receptor (FXR) plays an important role in physiological bile acid synthesis, secretion and transport. Defects of FXR regulation in these processes can cause cholestasis and subsequent pathological changes. FXR regulates the synthesis and uptake of bile acid via enzymes. It also increases bile acid solubility and elimination by promoting conjugation reactions and exports pump expression in cholestasis. The changes in bile acid transporters are involved in cholestasis, which can result from the mutations of transporter genes or acquired dysfunction of transport systems, such as inflammation-induced intrahepatic cholestasis. The modulation function of FXR in extrahepatic cholestasis is not identical to that in intrahepatic cholestasis, but the discrepancy may be reduced over time. In extrahepatic cholestasis, increasing biliary pressure can induce bile duct proliferation and bile infarcts, but the absence of FXR may ameliorate them. This review provides an update on the function of FXR in the regulation of bile acid metabolism, its role in the pathophysiological process of cholestasis and the therapeutic use of FXR agonists.
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Affiliation(s)
- Zhi Qing Yuan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ke Wei Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
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16
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Rajamanikandan S, Jeyakanthan J, Srinivasan P. Binding mode exploration of LuxR-thiazolidinedione analogues, e-pharmacophore-based virtual screening in the designing of LuxR inhibitors and its biological evaluation. J Biomol Struct Dyn 2016; 35:897-916. [PMID: 27141809 DOI: 10.1080/07391102.2016.1166455] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Master quorum sensing (QS) regulator LuxR of Vibrio harveyi is a unique member of the TetR protein superfamily. Recent studies have demonstrated the contribution of thiazolidinedione analogues in blocking QS by decreasing the DNA-binding ability of LuxR. However, the precise mechanism of thiazolidinedione analogues binding to LuxR is still unclear. In the present study, molecular docking combined with molecular dynamics (MD) simulations was performed to understand the mechanism of ligand binding to the protein. The binding pattern of thiazolidinedione analogues showed strong hydrogen bonding interactions with the amine group (NH) of polar amino acid residue Asn133 and carbonyl (C=O) interaction with negatively charged amino acid residue Gln137 in the binding site of LuxR. The stability of the protein-ligand complexes was confirmed by running 50 ns of MD simulations. Further, the four-featured pharmacophore hypothesis (AHHD) consists of one acceptor (A), two hydrophobic regions (HH) and one donor (D) group was used to screen compounds from ChemBridge database. The identified hit molecules were shown to have excellent pharmacokinetic properties under the acceptable range. Based on the computational studies, ChemBridge_5343641 was selected for in vitro assays. The 1-(4-chlorophenoxy)-3-[(4,6-dimethyl-2-pyrimidinyl)thio]-2-propanol (ChemBridge_5343641) showed significant reduction in bioluminescence in a dose-dependent manner. In addition, ChemBridge_5343641 inhibits biofilm formation and motility in V. harveyi. The result from the study suggests that ChemBridge_5343641 could serve as an anti-QS molecule.
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Affiliation(s)
| | - Jeyaraman Jeyakanthan
- a Department of Bioinformatics , Alagappa University , Karaikudi , TamilNadu , India
| | - Pappu Srinivasan
- a Department of Bioinformatics , Alagappa University , Karaikudi , TamilNadu , India.,b Department of Animal Health and Management , Alagappa University , Karaikudi , TamilNadu , India
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Per-Residue Energy Footprints-Based Pharmacophore Modeling as an Enhanced In Silico Approach in Drug Discovery: A Case Study on the Identification of Novel β-Secretase1 (BACE1) Inhibitors as Anti-Alzheimer Agents. Cell Mol Bioeng 2015. [DOI: 10.1007/s12195-015-0421-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Maity M, Dolui S, Maiti NC. Hydrogen bonding plays a significant role in the binding of coomassie brilliant blue-R to hemoglobin: FT-IR, fluorescence and molecular dynamics studies. Phys Chem Chem Phys 2015; 17:31216-27. [DOI: 10.1039/c5cp04661k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coomassie brilliant blue-R (CBB-R) specifically binds to bovine hemoglobin with a stoichiometric ratio of 1 : 1.
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Affiliation(s)
- Mritunjoy Maity
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- India
| | - Sandip Dolui
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- India
| | - Nakul C. Maiti
- Division of Structural Biology and Bioinformatics
- CSIR-Indian Institute of Chemical Biology
- India
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