1
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Grandits M, Ecker GF. Ligand- and Structure-based Approaches for Transmembrane Transporter Modeling. Curr Drug Res Rev 2024; 16:81-93. [PMID: 37157206 DOI: 10.2174/2589977515666230508123041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 05/10/2023]
Abstract
The study of transporter proteins is key to understanding the mechanism behind multidrug resistance and drug-drug interactions causing severe side effects. While ATP-binding transporters are well-studied, solute carriers illustrate an understudied family with a high number of orphan proteins. To study these transporters, in silico methods can be used to shed light on the basic molecular machinery by studying protein-ligand interactions. Nowadays, computational methods are an integral part of the drug discovery and development process. In this short review, computational approaches, such as machine learning, are discussed, which try to tackle interactions between transport proteins and certain compounds to locate target proteins. Furthermore, a few cases of selected members of the ATP binding transporter and solute carrier family are covered, which are of high interest in clinical drug interaction studies, especially for regulatory agencies. The strengths and limitations of ligand-based and structure-based methods are discussed to highlight their applicability for different studies. Furthermore, the combination of multiple approaches can improve the information obtained to find crucial amino acids that explain important interactions of protein-ligand complexes in more detail. This allows the design of drug candidates with increased activity towards a target protein, which further helps to support future synthetic efforts.
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Affiliation(s)
- Melanie Grandits
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
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2
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Romeo I, Brizzi A, Pessina F, Ambrosio FA, Aiello F, Belardo C, Carullo G, Costa G, De Petrocellis L, Frosini M, Luongo L, Maramai S, Paolino M, Moriello AS, Mugnaini C, Scorzelli F, Maione S, Corelli F, Di Marzo V, Alcaro S, Artese A. In Silico-Guided Rational Drug Design and Synthesis of Novel 4-(Thiophen-2-yl)butanamides as Potent and Selective TRPV1 Agonists. J Med Chem 2023; 66:6994-7015. [PMID: 37192374 DOI: 10.1021/acs.jmedchem.3c00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We describe an in silico-guided rational drug design and the synthesis of the suggested ligands, aimed at improving the TRPV1-ligand binding properties and the potency of N-(4-hydroxy-3-methoxybenzyl)-4-(thiophen-2-yl) butanamide I, a previously identified TRPV1 agonist. The docking experiments followed by molecular dynamics simulations and thermodynamic analysis led the drug design toward both the introduction of a lipophilic iodine and a flat pyridine/benzene at position 5 of the thiophene nucleus. Most of the synthesized compounds showed high TRPV1 efficacy and potency as well as selectivity. The molecular modeling analysis highlighted crucial hydrophobic interactions between Leu547 and the iodo-thiophene nucleus, as in amide 2a, or between Phe543 and the pyridinyl moiety, as in 3a. In the biological evaluation, both compounds showed protective properties against oxidative stress-induced ROS formation in human keratinocytes. Additionally, while 2a showed neuroprotective effects in both neurons and rat brain slices, 3a exhibited potent antinociceptive effect in vivo..
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Affiliation(s)
- Isabella Romeo
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Antonella Brizzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federica Pessina
- Dipartimento di Medicina Molecolare e dello Sviluppo, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Francesca Aiello
- Dipartimento di Farmacia e Scienza della Salute e della Nutrizione, Università della Calabria, Via P. Bucci, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Carmela Belardo
- Dipartimento di Medicina Sperimentale, Divisione di Farmacologia, Università degli Studi della Campania "L. Vanvitelli", |Via Costantinopoli 16, 80138 Napoli, Italy
| | - Gabriele Carullo
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Luciano De Petrocellis
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Comprensorio Olivetti, 80078 Pozzuoli, Napoli, Italy
| | - Maria Frosini
- Dipartimento di Scienze della Vita, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Livio Luongo
- Dipartimento di Medicina Sperimentale, Divisione di Farmacologia, Università degli Studi della Campania "L. Vanvitelli", |Via Costantinopoli 16, 80138 Napoli, Italy
| | - Samuele Maramai
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Aniello Schiano Moriello
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Comprensorio Olivetti, 80078 Pozzuoli, Napoli, Italy
- Epitech Group SpA, Via L. Einaudi 13, 35030 Saccolongo, Padova, Italy
| | - Claudia Mugnaini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Francesco Scorzelli
- Recipharm (Edmond Pharma), Strada Statale dei Giovi 131, 20037 Paderno Dugnano, Milano, Italy
| | - Sabatino Maione
- Dipartimento di Medicina Sperimentale, Divisione di Farmacologia, Università degli Studi della Campania "L. Vanvitelli", |Via Costantinopoli 16, 80138 Napoli, Italy
| | - Federico Corelli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, Comprensorio Olivetti, 80078 Pozzuoli, Napoli, Italy
- Heart and Lung Research Institute, Department of Medicine, Faculty of Medicine, and Institute of Nutrition and Functional Foods, NUTRISS Center, School of Nutrition, Faculty of Agriculture and Food Science, Université Laval, 2325 Rue de l'Université, Québec, Canada
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
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3
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Hsueh SCC, Aina A, Plotkin SS. Ensemble Generation for Linear and Cyclic Peptides Using a Reservoir Replica Exchange Molecular Dynamics Implementation in GROMACS. J Phys Chem B 2022; 126:10384-10399. [PMID: 36410027 DOI: 10.1021/acs.jpcb.2c05470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The profile of shapes presented by a cyclic peptide modulates its therapeutic efficacy and is represented by the ensemble of its sampled conformations. Although some algorithms excel at creating a diverse ensemble of cyclic peptide conformations, they seldom address the entropic contribution of flexible conformations and often have significant practical difficulty producing an ensemble with converged and reliable thermodynamic properties. In this study, an accelerated molecular dynamics (MD) method, namely, reservoir replica exchange MD (R-REMD or Res-REMD), was implemented in GROMACS ver. 4.6.7 and benchmarked on two small cyclic peptide model systems: a cyclized furin cleavage site of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (cyclo-(CGPRRARSG)) and oxytocin (disulfide-bonded CYIQNCPLG). Additionally, we also benchmarked Res-REMD on alanine dipeptide and Trpzip2 to demonstrate its validity and efficiency over REMD. For Trpzip2, Res-REMD coupled with an umbrella-sampling-derived reservoir generated similar folded fractions as regular REMD but on a much faster time scale. For cyclic peptides, Res-REMD appeared to be marginally faster than REMD in ensemble generation. Finally, Res-REMD was more effective in sampling rare events such as trans to cis peptide bond isomerization. We provide a GitHub page with the modified GROMACS source code for running Res-REMD at https://github.com/PlotkinLab/Reservoir-REMD.
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Affiliation(s)
- Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
| | - Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada.,Genome Science and Technology Program, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
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4
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Liu Z, Zubatiuk T, Roitberg A, Isayev O. Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials. J Chem Inf Model 2022; 62:5373-5382. [PMID: 36112860 DOI: 10.1021/acs.jcim.2c00817] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational programs accelerate the chemical discovery processes but often need proper three-dimensional molecular information as part of the input. Getting optimal molecular structures is challenging because it requires enumerating and optimizing a huge space of stereoisomers and conformers. We developed the Python-based Auto3D package for generating the low-energy 3D structures using SMILES as the input. Auto3D is based on state-of-the-art algorithms and can automatize the isomer enumeration and duplicate filtering process, 3D building process, geometry optimization, and ranking process. Tested on 50 molecules with multiple unspecified stereocenters, Auto3D is guaranteed to find the stereoconfiguration that yields the lowest-energy conformer. With Auto3D, we provide an extension of the ANI model. The new model, dubbed ANI-2xt, is trained on a tautomer-rich data set. ANI-2xt is benchmarked with DFT methods on geometry optimization and electronic and Gibbs free energy calculations. Compared with ANI-2x, ANI-2xt provides a 42% error reduction for tautomeric reaction energy calculations when using the gold-standard coupled-cluster calculation as the reference. ANI-2xt can accurately predict the energies and is several orders of magnitude faster than DFT methods.
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Affiliation(s)
- Zhen Liu
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania15213, United States
| | - Tetiana Zubatiuk
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania15213, United States
| | - Adrian Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania15213, United States
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5
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Abudayah A, Daoud S, Al-Sha'er M, Taha M. Pharmacophore Modeling of Targets Infested with Activity Cliffs via Molecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study. Mol Inform 2022; 41:e2200049. [PMID: 35973966 DOI: 10.1002/minf.202200049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Activity cliffs (ACs) are defined as pairs of structurally similar compounds with large difference in their potencies against certain biotarget. We recently proposed that potent AC members induce significant entropically-driven conformational modifications of the target that unveil additional binding interactions, while their weakly-potent counterparts are enthalpically-driven binders with little influence on the protein target. We herein propose to extract pharmacophores for ACs-infested target(s) from molecular dynamics (MD) frames of purely "enthalpic" potent binder(s) complexed within the particular target. Genetic function algorithm/machine learning (GFA/ML) can then be employed to search for the best possible combination of MD pharmacophore(s) capable of explaining bioactivity variations within a list of inhibitors. We compared the performance of this approach with established ligand-based and structure-based methods. Kinase inserts domain receptor (KDR) was used as a case study. KDR plays a crucial role in angiogenic signaling and its inhibitors have been approved in cancer treatment. Interestingly, GFA/ML selected, MD-based, pharmacophores were of comparable performances to ligand-based and structure-based pharmacophores. The resulting pharmacophores and QSAR models were used to capture hits from the national cancer institute list of compounds. The most active hit showed anti-KDR IC50 of 2.76 µM.
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Affiliation(s)
| | | | | | - Mutasem Taha
- Faculty of pharmacy,University of jordan, JORDAN
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6
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Targeting the actin nucleation promoting factor WASp provides a therapeutic approach for hematopoietic malignancies. Nat Commun 2021; 12:5581. [PMID: 34552085 PMCID: PMC8458504 DOI: 10.1038/s41467-021-25842-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer cells depend on actin cytoskeleton rearrangement to carry out hallmark malignant functions including activation, proliferation, migration and invasiveness. Wiskott–Aldrich Syndrome protein (WASp) is an actin nucleation-promoting factor and is a key regulator of actin polymerization in hematopoietic cells. The involvement of WASp in malignancies is incompletely understood. Since WASp is exclusively expressed in hematopoietic cells, we performed in silico screening to identify small molecule compounds (SMCs) that bind WASp and promote its degradation. We describe here one such identified molecule; this WASp-targeting SMC inhibits key WASp-dependent actin processes in several types of hematopoietic malignancies in vitro and in vivo without affecting naïve healthy cells. This small molecule demonstrates limited toxicity and immunogenic effects, and thus, might serve as an effective strategy to treat specific hematopoietic malignancies in a safe and precisely targeted manner. Cancer cells proliferate and invade via cytoskeletal proteins such as WASp, exclusively expressed in hematopoietic cells. Here the authors show a specific small molecule compound inhibiting cancer cell activity by WASp degradation and demonstrating its therapeutic potential in vitro and in vivo.
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7
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Zhang XR, Qiao YJ, Zhu HT, Kong QH, Wang D, Yang CR, Zhang YJ. Multiple in vitro biological effects of phenolic compounds from Terminalia chebula var. tomentella. JOURNAL OF ETHNOPHARMACOLOGY 2021; 275:114135. [PMID: 33892063 DOI: 10.1016/j.jep.2021.114135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/01/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Terminalia chebula (TC), a well-known Indian Ayurvedic medicine introduced into China in the Sui and Tang Dynasties, has been recorded and used medicinally as Fructus Chebulae, together with its variety tomentella (TCT) in the Chinese Pharmacopoeia. They have been also used commonly for the treatment of diabetes mellitus by Tibetan medicine. AIM OF THE STUDY To investigate the main bioactive and therapeutic principles in the fruits of TCT, based on the extensive evaluation of their anti-inflammatory and hypoglycemic activities. MATERIALS AND METHODS The TCT fresh fruits were analyzed by HPLC and separated further by column chromatography and preparative HPLC. The isolated compounds were identified by extensive spectroscopic analyses, including 1D/2D NMR, MS, UV, IR and ECD. Anti-inflammatory activity was evaluated by inhibition of NO production in RAW264.7 cells. The specific iNOS (PDB ID: 3E7G) structure was prepared by Discovery Studio 4.0, and the molecular docking simulation was performed on GOLD (version 5.2.2). Hypoglycemic activity was measured using the substrate solution of 4-nitrophenyl-α-d-glucopyranoside enzyme and buffer solution. RESULTS The HPLC analysis method of polyphenols in the fruits of TCT was established, and 13 main chromatographic peaks were identified, including six hydrolyzable tannins (2, 4-7, 10-11), three simple phenols (12-14), and one oleanane pentacyclic triterpene, arjungenin. Extensive chromatographic separation of TCT fresh fruits yielded 14 compounds, including one new natural hydrolyzable tannin, 2,3-(S)-HHDP-6-O-galloyl-d-glucose (1). The known compounds were identified as 10 hydrolyzable tannins (2-11) and three simple phenols (12-14). Compounds 10 (IC50 = 36.43 ± 0.21 μM), 11 (IC50 = 42.28 ± 0.09 μM) displayed stronger NO inhibitory activity than the positive control L-NMMA (IC50 = 42.34 ± 0.66 μM), while 2, 4, and 9 showed moderate inhibitory activity against NO production. Further molecular docking simulation of specific iNOS on 10 and 11, as well as five previously isolated lignans 15-19 showed that there were no obvious rules between docking results and the in vitro NO inhibitory activity for hydrolyzable tannins (10 and 11), while the mechanism of anti-inflammatory activity for lignans was related to the substitution of conjugated aldehyde groups. Moreover, most of the hydrolyzable tannins (1-2, 4-5, 9-11) and simple phenol (12) displayed stronger inhibitory effects on α-glucosidase than the positive control, quercetin (IC50 = 6.118 ± 0.071 μM), with IC50 values ranging from 0.079 to 16.494 μM. Among these bioactive isolates, the hydrolyzable tannins 2, 4-5, and 9-11, and simple phenol 12 are major chemical components in TCT fruit. CONCLUSIONS The results showed that lignans and hydrolyzed tannins are the main active ingredients of TCT fruits, responsible for the traditional treatment of sore throat and cough. Moreover, hydrolyzed tannins and simple phenolic compounds with potential hypoglycemic activity are closely related to the ethno-pharmacological uses of TCT fruits on diabetes in Tibetan medicine.
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Affiliation(s)
- Xiao-Rui Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yi-Jun Qiao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Hong-Tao Zhu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Qing-Hua Kong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Dong Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Chong-Ren Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Ying-Jun Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China; Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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8
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Tong J, Zhao S. Large-Scale Analysis of Bioactive Ligand Conformational Strain Energy by Ab Initio Calculation. J Chem Inf Model 2021; 61:1180-1192. [PMID: 33630603 DOI: 10.1021/acs.jcim.0c01197] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ligand conformational strain energy (LCSE) plays an important role in virtual screening and lead optimization. While various studies have provided insights into LCSE for small-molecule ligands in the Protein Data Bank (PDB), conclusions are inconsistent mainly due to small datasets, poor quality control of crystal structures, and molecular mechanics (MM) or low-level quantum mechanics (QM) calculations. Here, we built a high-quality dataset (LigBoundConf) of 8145 ligand-bound conformations from PDB crystal structures and calculated LCSE at the M062X-D3/ma-TZVPP (SMD)//M062X-D3/def2-SVP(SMD) level for each case in the dataset. The mean/median LCSE is 4.6/3.7 kcal/mol for 6672 successfully calculated cases, which is significantly lower than the estimates based on molecular mechanics in many previous analyses. Especially, when removing ligands with nonaromatic ring(s) that are prone to have large LCSEs due to electron density overfitting, the mean/median LCSE was reduced to 3.3/2.5 kcal/mol. We further reveal that LCSE is correlated with several ligand properties, including formal atomic charge, molecular weight, number of rotatable bonds, and number of hydrogen-bond donors and acceptors. In addition, our results show that although summation of torsion strains is a good approximation of LCSE for most cases, for a small fraction (about 6%) of our dataset, it underestimates LCSEs if ligands could form nonlocal intramolecular interactions in the unbound state. Taken together, our work provides a comprehensive profile of LCSE for ligands in PDB, which could help ligand conformation generation, ligand docking pose evaluation, and lead optimization.
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Affiliation(s)
- Jiahui Tong
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.,University of Chinese Academy of Sciences, No. 19A, Yuquan Road, Beijing 100049, China.,Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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9
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Jiang H, Fan M, Wang J, Sarma A, Mohanty S, Dokholyan NV, Mahdavi M, Kandemir MT. Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks. J Chem Inf Model 2020; 60:4594-4602. [PMID: 33100014 PMCID: PMC10706896 DOI: 10.1021/acs.jcim.0c00542] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The high-performance computational techniques have brought significant benefits for drug discovery efforts in recent decades. One of the most challenging problems in drug discovery is the protein-ligand binding pose prediction. To predict the most stable structure of the complex, the performance of conventional structure-based molecular docking methods heavily depends on the accuracy of scoring or energy functions (as an approximation of affinity) for each pose of the protein-ligand docking complex to effectively guide the search in an exponentially large solution space. However, due to the heterogeneity of molecular structures, the existing scoring calculation methods are either tailored to a particular data set or fail to exhibit high accuracy. In this paper, we propose a convolutional neural network (CNN)-based model that learns to predict the stability factor of the protein-ligand complex and exhibits the ability of CNNs to improve the existing docking software. Evaluated results on PDBbind data set indicate that our approach reduces the execution time of the traditional docking-based method while improving the accuracy. Our code, experiment scripts, and pretrained models are available at https://github.com/j9650/MedusaNet.
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Affiliation(s)
- Huaipan Jiang
- Department of Computer Science and Engineering, Pennsylvania State University, State College 16802, United States
| | - Mengran Fan
- Department of Computer Science and Engineering, Pennsylvania State University, State College 16802, United States
| | - Jian Wang
- Departments of Pharmacology and Biochemistry and Molecular Biology, Pennsylvania State College of Medicine, Hershey 17033, United States
| | - Anup Sarma
- Department of Computer Science and Engineering, Pennsylvania State University, State College 16802, United States
| | - Shruti Mohanty
- Department of Computer Science and Engineering, Pennsylvania State University, State College 16802, United States
| | - Nikolay V Dokholyan
- Departments of Pharmacology and Biochemistry and Molecular Biology, Pennsylvania State College of Medicine, Hershey 17033, United States
- Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, State College 16802, United States
| | - Mehrdad Mahdavi
- Department of Computer Science and Engineering, Pennsylvania State University, State College 16802, United States
| | - Mahmut T Kandemir
- Department of Computer Science and Engineering, Pennsylvania State University, State College 16802, United States
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10
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Mancini G, Fusè M, Lazzari F, Chandramouli B, Barone V. Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm. J Chem Phys 2020; 153:124110. [DOI: 10.1063/5.0018314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Federico Lazzari
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
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11
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Zalloum H, AbuThiab T, Hameduh T, AlBayyari S, Zalloum W, Abu-Irmaileh B, Mubarak MS, Zihlif M. Comparative anti-proliferative effects of potential HER2 inhibitors on a panel of breast cancer cell lines. Breast Cancer 2019; 27:213-224. [PMID: 31559601 DOI: 10.1007/s12282-019-01011-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/14/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Breast cancer is one of the most lethal types of cancer in women worldwide. The human epidermal growth factor receptor 2 (HER2) is considered as a validated target in breast cancer therapy. Previously, we have used quantitative structure activity relationship QSAR equations and their associated pharmacophore models to screen for new promising HER2 structurally diverse inhibitory leads which were tested against HER2-overexpressing SKOV3 ovarian cancer cell line. OBJECTIVE In this study, we sought to explore the effect of most active ligands against different normal and breast cancer cell lines that represent different breast cancer subtypes with distinguished expression levels in HER2 and HER1. METHODS We have tested the promising compounds against SKBR3, MDA-MB-231, MCF7, human fibroblast, and MCF10 cell lines. To understand the inhibitory effects of the active ligands against HER2 over expressed breast cancer cell lines, all inhibitors and the control compound, lapatinib, were docked into the active site of HER2 enzyme performed using Ligand Fit docking engine and PMF scoring function. RESULTS Five ligands exhibited promising results with relatively low IC50 values on cells that amplify HER2 and high IC50 on those that do not express such a receptor. The most potent compound (compound 13) showed an IC50 of 0.046 µM. To test their toxicity against normal cells, the active compounds were tested against both normal fibroblast and normal breast cancer cell MCF-10 and relatively high IC50 values were scored. The IC50 values on HER2 over-expressed breast cancer and normal fibroblast cells provided a promising safety index. Docking results showed the highest similarity in the binding site between the most active ligand and the lapatinib. CONCLUSION Our pharmacophore model resulted in a high potent ligand that shows high potency against HER2 positive breast cancer and relatively low toxicity towards the normal human cells.
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Affiliation(s)
- Hiba Zalloum
- Hamdi Mango Research Center for Scientific Research, The University of Jordan, Amman, 11942, Jordan.
| | - Tuka AbuThiab
- Hamdi Mango Research Center for Scientific Research, The University of Jordan, Amman, 11942, Jordan
| | - Tareq Hameduh
- Hamdi Mango Research Center for Scientific Research, The University of Jordan, Amman, 11942, Jordan
| | - Sara AlBayyari
- Hamdi Mango Research Center for Scientific Research, The University of Jordan, Amman, 11942, Jordan
| | - Waleed Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O. Box 2882, Amman, 11821, Jordan
| | - Basha'er Abu-Irmaileh
- Hamdi Mango Research Center for Scientific Research, The University of Jordan, Amman, 11942, Jordan
| | - Mohammad S Mubarak
- Department of Chemistry, Faculty of Science, The University of Jordan, Amman, 11942, Jordan
| | - Malek Zihlif
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman, 11942, Jordan.
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12
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Marchand DJJ, Noori M, Roberts A, Rosenberg G, Woods B, Yildiz U, Coons M, Devore D, Margl P. A Variable Neighbourhood Descent Heuristic for Conformational Search Using a Quantum Annealer. Sci Rep 2019; 9:13708. [PMID: 31548549 PMCID: PMC6757033 DOI: 10.1038/s41598-019-47298-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/01/2019] [Indexed: 11/24/2022] Open
Abstract
Discovering the low-energy conformations of a molecule is of great interest to computational chemists, with applications in in silico materials design and drug discovery. In this paper, we propose a variable neighbourhood search heuristic for the conformational search problem. Using the structure of a molecule, neighbourhoods are chosen to allow for the efficient use of a binary quadratic optimizer for conformational search. The method is flexible with respect to the choice of molecular force field and the number of discretization levels in the search space, and can be further generalized to take advantage of higher-order binary polynomial optimizers. It is well-suited for the use of devices such as quantum annealers. After carefully defining neighbourhoods, the method easily adapts to the size and topology of these devices, allowing for seamless scaling alongside their future improvements.
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Affiliation(s)
- D J J Marchand
- 1QB Information Technologies (1QBit), 458-550 Burrard Street, Vancouver, BC, V6C 2B5, Canada
| | - M Noori
- 1QB Information Technologies (1QBit), 458-550 Burrard Street, Vancouver, BC, V6C 2B5, Canada.
| | - A Roberts
- 1QB Information Technologies (1QBit), 458-550 Burrard Street, Vancouver, BC, V6C 2B5, Canada
| | - G Rosenberg
- 1QB Information Technologies (1QBit), 458-550 Burrard Street, Vancouver, BC, V6C 2B5, Canada
| | - B Woods
- 1QB Information Technologies (1QBit), 458-550 Burrard Street, Vancouver, BC, V6C 2B5, Canada
| | - U Yildiz
- 1QB Information Technologies (1QBit), 458-550 Burrard Street, Vancouver, BC, V6C 2B5, Canada
| | - M Coons
- The Dow Chemical Company, Core R&D, 1776 Building, Midland, MI, 48674, United States
| | - D Devore
- The Dow Chemical Company, Core R&D, 1776 Building, Midland, MI, 48674, United States
| | - P Margl
- The Dow Chemical Company, Core R&D, 1776 Building, Midland, MI, 48674, United States
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13
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Morello E, Pérez-Berezo T, Boisseau C, Baranek T, Guillon A, Bréa D, Lanotte P, Carpena X, Pietrancosta N, Hervé V, Ramphal R, Cenac N, Si-Tahar M. Pseudomonas aeruginosa Lipoxygenase LoxA Contributes to Lung Infection by Altering the Host Immune Lipid Signaling. Front Microbiol 2019; 10:1826. [PMID: 31474948 PMCID: PMC6702342 DOI: 10.3389/fmicb.2019.01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/24/2019] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacteria and a major cause of nosocomial pneumonia. P. aeruginosa has many virulence factors contributing to its ability to colonize the host. LoxA is a lipoxygenase enzyme secreted by P. aeruginosa that oxidizes polyunsaturated fatty acids. Based on previous in vitro biochemical studies, several biological roles of LoxA have been hypothesized, including interference of the host lipid signaling, and modulation of bacterial invasion properties. However, the contribution of LoxA to P. aeruginosa lung pathogenesis per se remained unclear. In this study, we used complementary in vitro and in vivo approaches, clinical strains of P. aeruginosa as well as lipidomics technology to investigate the role of LoxA in lung infection. We found that several P. aeruginosa clinical isolates express LoxA. When secreted in the lungs, LoxA processes a wide range of host polyunsaturated fatty acids, which further results in the production of bioactive lipid mediators (including lipoxin A4). LoxA also inhibits the expression of major chemokines (e.g., MIPs and KC) and the recruitment of key leukocytes. Remarkably, LoxA promotes P. aeruginosa persistence in lungs tissues. Hence, our study suggests that LoxA-dependent interference of the host lipid pathways may contribute to P. aeruginosa lung pathogenesis.
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Affiliation(s)
- Eric Morello
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Teresa Pérez-Berezo
- Institut de Recherche en Santé Digestive, Université de Toulouse, INSERM, INRA, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Chloé Boisseau
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Thomas Baranek
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Antoine Guillon
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Déborah Bréa
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Philippe Lanotte
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France.,Université de Tours, UMR1282 ISP, Faculté de Médecine, Equipe Bactéries et Risque Materno-Foetal, Tours, France
| | - Xavier Carpena
- Institut de Biologia Molecular de Barcelona, Parc Científic de Barcelona, Barcelona, Spain.,XALOC Beamline, ALBA Synchrotron, Cerdanyola del Vallès, Spain
| | - Nicolas Pietrancosta
- Plateau 2MI, CNRS UMR8601, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Centre Universitaire des Saints-Pères, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Virginie Hervé
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
| | - Reuben Ramphal
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France.,Department of Medicine, University of Florida, Gainesville, FL, United States
| | - Nicolas Cenac
- Institut de Recherche en Santé Digestive, Université de Toulouse, INSERM, INRA, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Mustapha Si-Tahar
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France.,Université de Tours, Tours, France
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14
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Choudhury C, Narahari Sastry G. Pharmacophore Modelling and Screening: Concepts, Recent Developments and Applications in Rational Drug Design. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [DOI: 10.1007/978-3-030-05282-9_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Energy windows for computed compound conformers: covering artefacts or truly large reorganization energies? Future Med Chem 2019; 11:97-118. [DOI: 10.4155/fmc-2018-0400] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The generation of 3D conformers of small molecules underpins most computational drug discovery. Thus, the conformer quality is critical and depends on their energetics. A key parameter is the empirical conformational energy window (ΔEw), since only conformers within ΔEw are retained. However, ΔEw values in use appear unrealistically large. We analyze the factors pertaining to the conformer energetics and ΔEw. We argue that more attention must be focused on the problem of collapsed low-energy conformers. That is due to artificial intramolecular stabilization and occurs even with continuum solvation. Consequently, the conformational energy of extended bioactive structures is artefactually increased, which inflates ΔEw. Thus, this Perspective highlights the issues arising from low-energy conformers and suggests improvements via empirical or physics-based strategies.
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16
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Manhas A, Lone MY, Jha PC. In search of the representative pharmacophore hypotheses of the enzymatic proteome of Plasmodium falciparum: a multicomplex-based approach. Mol Divers 2018; 23:453-470. [DOI: 10.1007/s11030-018-9885-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/06/2018] [Indexed: 01/17/2023]
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17
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Li Y, Peng J, Zhou Y, Li P, Li Y, Liu X, Siddique AN, Zhang L, Zuo Z. Pharmacophore modeling, molecular docking and molecular dynamics simulations toward identifying lead compounds for Chk1. Comput Biol Chem 2018; 76:53-60. [DOI: 10.1016/j.compbiolchem.2018.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/29/2018] [Accepted: 06/03/2018] [Indexed: 10/14/2022]
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18
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Cavasin AT, Hillisch A, Uellendahl F, Schneckener S, Göller AH. Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water. J Chem Inf Model 2018; 58:1005-1020. [PMID: 29717870 DOI: 10.1021/acs.jcim.8b00151] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prediction of compound properties from structure via quantitative structure-activity relationship and machine-learning approaches is an important computational chemistry task in small-molecule drug research. Though many such properties are dependent on three-dimensional structures or even conformer ensembles, the majority of models are based on descriptors derived from two-dimensional structures. Here we present results from a thorough benchmark study of force field, semiempirical, and density functional methods for the calculation of conformer energies in the gas phase and water solvation as a foundation for the correct identification of relevant low-energy conformers. We find that the tight-binding ansatz GFN-xTB shows the lowest error metrics and highest correlation to the benchmark PBE0-D3(BJ)/def2-TZVP in the gas phase for the computationally fast methods and that in solvent OPLS3 becomes comparable in performance. MMFF94, AM1, and DFTB+ perform worse, whereas the performance-optimized but far more expensive functional PBEh-3c yields energies almost perfectly correlated to the benchmark and should be used whenever affordable. On the basis of our findings, we have implemented a reliable and fast protocol for the identification of low-energy conformers of drug-like molecules in water that can be used for the quantification of strain energy and entropy contributions to target binding as well as for the derivation of conformer-ensemble-dependent molecular descriptors.
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Affiliation(s)
| | - Alexander Hillisch
- Bayer AG , Drug Discovery, Chemical Research , 42096 Wuppertal , Germany
| | - Felix Uellendahl
- Bayer AG , Drug Discovery, Chemical Research , 42096 Wuppertal , Germany
| | - Sebastian Schneckener
- Bayer AG , Engineering & Technology, Applied Mathematics , 51368 Leverkusen , Germany
| | - Andreas H Göller
- Bayer AG , Drug Discovery, Chemical Research , 42096 Wuppertal , Germany
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19
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Exploration of Mycobacterium tuberculosis structural proteome: An in-silico approach. J Theor Biol 2018; 439:14-23. [DOI: 10.1016/j.jtbi.2017.11.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 07/19/2017] [Accepted: 11/28/2017] [Indexed: 12/20/2022]
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20
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Dreher J, Scheiber J, Stiefl N, Baumann K. xMaP-An Interpretable Alignment-Free Four-Dimensional Quantitative Structure-Activity Relationship Technique Based on Molecular Surface Properties and Conformer Ensembles. J Chem Inf Model 2018; 58:165-181. [PMID: 29172519 DOI: 10.1021/acs.jcim.7b00419] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel alignment-free molecular descriptor called xMaP (flexible MaP descriptor) is introduced. The descriptor is the advancement of the previously published translationally and rotationally invariant three-dimensional (3D) descriptor MaP (mapping property distributions onto the molecular surface) to the fourth dimension (4D). In addition to MaP, xMaP is independent of the chosen starting conformation of the encoded molecules and is therefore entirely alignment-free. This is achieved by using ensembles of conformers, which are generated by conformational searches. This step of the procedure is similar to Hopfinger's 4D quantitative structure-activity relationship (QSAR). A five-step procedure is used to compute the xMaP descriptor. First, a conformational search for each molecule is carried out. Next, for each of the conformers an approximation to the molecular surface with equally distributed surface points is computed. Third, molecular properties are projected onto this surface. Fourth, areas of identical properties are clustered to so-called patches. Fifth, the spatial distribution of the patches is converted into an alignment-free descriptor that is based on the entire conformer ensemble. The resulting descriptor can be interpreted by superimposing the most important descriptor variables and the molecules of the data set. The most important descriptor variables are identified with chemometric regression tools. The novel descriptor was applied to several benchmark data sets and was compared to other descriptors and QSAR techniques comprising a binary fingerprint, a topological pharmacophore descriptor (Cats2D), and the field-based 3D-QSAR technique GRID/PLS which is alignment-dependent. The use of conformer ensembles renders xMaP very robust. It turns out that xMaP performs very well on (almost) all data sets and that the statistical results are comparable to GRID/PLS. In addition to that, xMaP can also be used to efficiently visualize the derived quantitative structure-activity relationships.
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Affiliation(s)
- Jan Dreher
- Institute of Medicinal and Pharmaceutical Chemistry, University of Technology Braunschweig , Beethovenstrasse 55, D 38106 Braunschweig, Germany
| | - Josef Scheiber
- Institute of Medicinal and Pharmaceutical Chemistry, University of Technology Braunschweig , Beethovenstrasse 55, D 38106 Braunschweig, Germany
| | - Nikolaus Stiefl
- Institute of Medicinal and Pharmaceutical Chemistry, University of Technology Braunschweig , Beethovenstrasse 55, D 38106 Braunschweig, Germany
| | - Knut Baumann
- Institute of Medicinal and Pharmaceutical Chemistry, University of Technology Braunschweig , Beethovenstrasse 55, D 38106 Braunschweig, Germany
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21
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Passeri GI, Trisciuzzi D, Alberga D, Siragusa L, Leonetti F, Mangiatordi GF, Nicolotti O. Strategies of Virtual Screening in Medicinal Chemistry. ACTA ACUST UNITED AC 2018. [DOI: 10.4018/ijqspr.2018010108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virtual screening represents an effective computational strategy to rise-up the chances of finding new bioactive compounds by accelerating the time needed to move from an initial intuition to market. Classically, the most pursued approaches rely on ligand- and structure-based studies, the former employed when structural data information about the target is missing while the latter employed when X-ray/NMR solved or homology models are instead available for the target. The authors will focus on the most advanced techniques applied in this area. In particular, they will survey the key concepts of virtual screening by discussing how to properly select chemical libraries, how to make database curation, how to applying and- and structure-based techniques, how to wisely use post-processing methods. Emphasis will be also given to the most meaningful databases used in VS protocols. For the ease of discussion several examples will be presented.
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Affiliation(s)
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Domenico Alberga
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Lydia Siragusa
- Molecular Discovery Ltd., Pinner, Middlesex, London, United Kingdom
| | - Francesco Leonetti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Giuseppe F. Mangiatordi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
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22
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Wang L, Coric P, Zhu K, Liu WQ, Vidal M, Bouaziz S, Broussy S. Synthesis and characterization of water-soluble macrocyclic peptides stabilizing protein α-turn. Org Biomol Chem 2018; 16:459-471. [DOI: 10.1039/c7ob02852k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Macrocyclic peptides mimic tight “non-classical” α-turn type II-αLS found in proteins, as shown by spectroscopic and computational analysis of their equilibrating conformations.
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Affiliation(s)
- Lei Wang
- UMR COMETE 8638 CNRS
- Université Paris Descartes
- Faculté de Pharmacie de Paris
- Sorbonne Paris Cité
- Paris 75006
| | - Pascale Coric
- UMR 8015 CNRS
- Université Paris Descartes
- Faculté de Pharmacie de Paris
- Sorbonne Paris Cité
- Paris 75006
| | - Kexin Zhu
- UMR COMETE 8638 CNRS
- Université Paris Descartes
- Faculté de Pharmacie de Paris
- Sorbonne Paris Cité
- Paris 75006
| | - Wang-Qing Liu
- UMR COMETE 8638 CNRS
- Université Paris Descartes
- Faculté de Pharmacie de Paris
- Sorbonne Paris Cité
- Paris 75006
| | - Michel Vidal
- UMR COMETE 8638 CNRS
- Université Paris Descartes
- Faculté de Pharmacie de Paris
- Sorbonne Paris Cité
- Paris 75006
| | - Serge Bouaziz
- UMR 8015 CNRS
- Université Paris Descartes
- Faculté de Pharmacie de Paris
- Sorbonne Paris Cité
- Paris 75006
| | - Sylvain Broussy
- UMR COMETE 8638 CNRS
- Université Paris Descartes
- Faculté de Pharmacie de Paris
- Sorbonne Paris Cité
- Paris 75006
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23
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Peach ML, Cachau RE, Nicklaus MC. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. J Mol Recognit 2017; 30:10.1002/jmr.2618. [PMID: 28233410 PMCID: PMC5553890 DOI: 10.1002/jmr.2618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/25/2022]
Abstract
In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures. The main source of disagreement between different analyses appears to be due to divergent treatments of electrostatics and solvation. At the same time, however, for many ligands, a high conformational energy is in error, due to either crystal structure inaccuracies or incorrect determination of the reference state. Aside from simple chemistry mistakes, we argue that crystal structure error may mainly be because of the heuristic weighting of ligand stereochemical restraints relative to the fit of the structure to the electron density. This problem cannot be fixed with improvements to electron density fitting or with simple ligand geometry checks, though better metrics are needed for evaluating ligand and binding site chemistry in addition to geometry during structure refinement. The ultimate solution for accurately determining ligand conformational energies lies in ultrahigh-resolution crystal structures that can be refined without restraints.
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Affiliation(s)
- Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raul E Cachau
- Data Science and Information Technology Program, Advanced Biomedical Computing Center, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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24
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Sommer T, Hübner H, El Kerdawy A, Gmeiner P, Pischetsrieder M, Clark T. Identification of the Beer Component Hordenine as Food-Derived Dopamine D2 Receptor Agonist by Virtual Screening a 3D Compound Database. Sci Rep 2017; 7:44201. [PMID: 28281694 PMCID: PMC5345022 DOI: 10.1038/srep44201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/06/2017] [Indexed: 01/11/2023] Open
Abstract
The dopamine D2 receptor (D2R) is involved in food reward and compulsive food intake. The present study developed a virtual screening (VS) method to identify food components, which may modulate D2R signalling. In contrast to their common applications in drug discovery, VS methods are rarely applied for the discovery of bioactive food compounds. Here, databases were created that exclusively contain substances occurring in food and natural sources (about 13,000 different compounds in total) as the basis for combined pharmacophore searching, hit-list clustering and molecular docking into D2R homology models. From 17 compounds finally tested in radioligand assays to determine their binding affinities, seven were classified as hits (hit rate = 41%). Functional properties of the five most active compounds were further examined in β-arrestin recruitment and cAMP inhibition experiments. D2R-promoted G-protein activation was observed for hordenine, a constituent of barley and beer, with approximately identical ligand efficacy as dopamine (76%) and a Ki value of 13 μM. Moreover, hordenine antagonised D2-mediated β-arrestin recruitment indicating functional selectivity. Application of our databases provides new perspectives for the discovery of bioactive food constituents using VS methods. Based on its presence in beer, we suggest that hordenine significantly contributes to mood-elevating effects of beer.
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Affiliation(s)
- Thomas Sommer
- Computer Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
- Food Chemistry Unit, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Ahmed El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr-el-Aini Street, Cairo, P. O. Box 11562, Egypt
- Molecular Modeling Unit, Faculty of Pharmacy, Cairo University, Kasr-el-Aini Street, Cairo, P. O. Box 11562, Egypt
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Monika Pischetsrieder
- Food Chemistry Unit, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Timothy Clark
- Computer Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
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25
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Sun H, Wang D, Song X, Zhang Y, Ding W, Peng X, Zhang X, Li Y, Ma Y, Wang R, Yu P. Natural Prenylchalconaringenins and Prenylnaringenins as Antidiabetic Agents: α-Glucosidase and α-Amylase Inhibition and in Vivo Antihyperglycemic and Antihyperlipidemic Effects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1574-1581. [PMID: 28132506 DOI: 10.1021/acs.jafc.6b05445] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Inhibition of α-glucosidase and α-amylase decreases postprandial blood glucose levels and delays glucose absorption, making it a treatment strategy for type 2 diabetes. This study examined in vivo and in vitro antidiabetic activities of natural prenylchalconaringenins 1 and 2 and prenylnaringenins 3 and 4, found in hops and beer. 3'-Geranylchalconaringenin (2) competitively and irreversibly inhibited α-glucosidase (IC50 = 1.08 μM) with activity 50-fold higher than that of acarbose (IC50 = 51.30 μM) and showed moderate inhibitory activity against α-amylase (IC50 = 20.46 μM). Docking analysis substantiated these findings. In addition, compound 2 suppressed the increase in postprandial blood glucose levels and serum levels of total cholesterol and triglycerides in streptozotocin-induced diabetic mice. Taken together, these results suggest that 2 has dual inhibitory activity against α-glucosidase and α-amylase and alleviates diabetic hyperglycemia and hyperlipidemia, making it a potential functional food ingredient and drug candidate for management of type 2 diabetes.
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Affiliation(s)
- Hua Sun
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Dong Wang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Xiaotong Song
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Yazhou Zhang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Weina Ding
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Xiaolin Peng
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Xiaoting Zhang
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Yashan Li
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
| | - Ying Ma
- School of Pharmacy, Tianjin Medical University , Tianjin 300070, China
| | - Runling Wang
- School of Pharmacy, Tianjin Medical University , Tianjin 300070, China
| | - Peng Yu
- China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, Tianjin University of Science and Technology , Tianjin 300457, China
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26
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Friedrich NO, Meyder A, de Bruyn Kops C, Sommer K, Flachsenberg F, Rarey M, Kirchmair J. High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. J Chem Inf Model 2017; 57:529-539. [PMID: 28206754 DOI: 10.1021/acs.jcim.6b00613] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a cheminformatics pipeline for the fully automated selection and extraction of high-quality protein-bound ligand conformations from X-ray structural data. The pipeline evaluates the validity and accuracy of the 3D structures of small molecules according to multiple criteria, including their fit to the electron density and their physicochemical and structural properties. Using this approach, we compiled two high-quality datasets from the Protein Data Bank (PDB): a comprehensive dataset and a diversified subset of 4626 and 2912 structures, respectively. The datasets were applied to benchmarking seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK. Substantial differences in the performance of the individual algorithms were observed, with RDKit and ETKDG generally achieving a favorable balance of accuracy, ensemble size and runtime. The Platinum datasets are available for download from http://www.zbh.uni-hamburg.de/platinum_dataset .
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Affiliation(s)
- Nils-Ole Friedrich
- University of Hamburg , ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg 20146, Germany
| | - Agnes Meyder
- University of Hamburg , ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg 20146, Germany
| | - Christina de Bruyn Kops
- University of Hamburg , ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg 20146, Germany
| | - Kai Sommer
- University of Hamburg , ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg 20146, Germany
| | - Florian Flachsenberg
- University of Hamburg , ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg 20146, Germany
| | - Matthias Rarey
- University of Hamburg , ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg 20146, Germany
| | - Johannes Kirchmair
- University of Hamburg , ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg 20146, Germany
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27
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Dhers L, Pietrancosta N, Ducassou L, Ramassamy B, Dairou J, Jaouen M, André F, Mansuy D, Boucher JL. Spectral and 3D model studies of the interaction of orphan human cytochrome P450 2U1 with substrates and ligands. Biochim Biophys Acta Gen Subj 2017; 1861:3144-3153. [DOI: 10.1016/j.bbagen.2016.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/06/2016] [Accepted: 07/21/2016] [Indexed: 02/08/2023]
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28
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Wang Q, Sciabola S, Barreiro G, Hou X, Bai G, Shapiro MJ, Koehn F, Villalobos A, Jacobson MP. Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. J Chem Inf Model 2016; 56:2194-2206. [PMID: 27731994 DOI: 10.1021/acs.jcim.6b00237] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrocycles pose challenges for computer-aided drug design due to their conformational complexity. One fundamental challenge is identifying all low-energy conformations of the macrocyclic ring, which is important for modeling target binding, passive membrane permeation, and other conformation-dependent properties. Macrocyclic polyketides are medically and biologically important natural products characterized by structural and functional diversity. Advances in synthetic biology and semisynthetic methods may enable creation of an even more diverse set of non-natural product polyketides for drug discovery and other applications. However, the conformational sampling of these flexible compounds remains demanding. We developed and optimized a dihedral angle-based macrocycle conformational sampling method for macrocycles of arbitrary structure, and here we apply it to diverse polyketide natural products. First, we evaluated its performance using a data set of 37 polyketides with available crystal structures, with 9-22 rotatable bonds in the macrocyclic ring. Our optimized protocol was able to reproduce the crystal structure of polyketides' aglycone backbone within 0.50 Å RMSD for 31 out of 37 polyketides. Consistent with prior structural studies, our analysis suggests that polyketides tend to have multiple distinct low-energy structures, including the bioactive (target-bound) conformation as well as others of unknown significance. For this reason, we also introduce a strategy to improve both efficiency and accuracy of the conformational search by utilizing torsional restraints derived from NMR vicinal proton couplings to restrict the conformational search. Finally, as a first application of the method, we made blinded predictions of the passive membrane permeability of a diverse set of polyketides, based on their predicted structures in low- and high-dielectric media.
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Affiliation(s)
- Qin Wang
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - Simone Sciabola
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Gabriela Barreiro
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Xinjun Hou
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | | | | | | | - Anabella Villalobos
- Neuroscience and Pain Medicinal Chemistry, Pfizer Worldwide Research and Development , Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
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29
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Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures. Drug Discov Today 2016; 21:1672-1680. [DOI: 10.1016/j.drudis.2016.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 06/21/2016] [Indexed: 12/27/2022]
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30
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Aiello F, Badolato M, Pessina F, Sticozzi C, Maestrini V, Aldinucci C, Luongo L, Guida F, Ligresti A, Artese A, Allarà M, Costa G, Frosini M, Schiano Moriello A, De Petrocellis L, Valacchi G, Alcaro S, Maione S, Di Marzo V, Corelli F, Brizzi A. Design and Synthesis of New Transient Receptor Potential Vanilloid Type-1 (TRPV1) Channel Modulators: Identification, Molecular Modeling Analysis, and Pharmacological Characterization of the N-(4-Hydroxy-3-methoxybenzyl)-4-(thiophen-2-yl)butanamide, a Small Molecule Endowed with Agonist TRPV1 Activity and Protective Effects against Oxidative Stress. ACS Chem Neurosci 2016; 7:737-48. [PMID: 26942555 DOI: 10.1021/acschemneuro.5b00333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
4-(Thiophen-2-yl)butanoic acid was identified as a cyclic substitute of the unsaturated alkyl chain of the natural ligand, capsaicin. Accordingly, a new class of amides was synthesized in good yield and high purity and their molecular recognition against the target was investigated by means of docking experiments followed by molecular dynamics simulations, in order to rationalize their geometrical and thermodynamic profiles. The pharmacological properties of these new compounds were expressed as activation (EC50) and desensitization (IC50) potencies. Several compounds were found to activate TRPV1 channels, and in particular, derivatives 1 and 10 behaved as TRPV1 agonists endowed with good efficacy as compared to capsaicin. The most promising compound 1 was also evaluated for its protective role against oxidative stress on keratinocytes and differentiated human neuroblastoma cell lines expressing the TRPV1 receptor as well as for its cytotoxicity and analgesic activity in vivo.
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Affiliation(s)
- Francesca Aiello
- Dipartimento
di Farmacia e Scienza della Salute e della Nutrizione, Università della Calabria, Edificio Polifunzionale, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Mariateresa Badolato
- Dipartimento
di Farmacia e Scienza della Salute e della Nutrizione, Università della Calabria, Edificio Polifunzionale, 87036 Arcavacata di Rende, Cosenza, Italy
| | | | - Claudia Sticozzi
- Dipartimento
Scienza della Vita e Biotecnologie, Università degli Studi di Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy
| | | | | | - Livio Luongo
- Dipartimento
di Medicina Sperimentale, Sezione di Farmacologia “L. Donatelli”, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Francesca Guida
- Dipartimento
di Medicina Sperimentale, Sezione di Farmacologia “L. Donatelli”, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Alessia Ligresti
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Anna Artese
- Dipartimento
di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Marco Allarà
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Giosué Costa
- Dipartimento
di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | | | - Aniello Schiano Moriello
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Luciano De Petrocellis
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Giuseppe Valacchi
- Dipartimento
Scienza della Vita e Biotecnologie, Università degli Studi di Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy
| | - Stefano Alcaro
- Dipartimento
di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Sabatino Maione
- Dipartimento
di Medicina Sperimentale, Sezione di Farmacologia “L. Donatelli”, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Vincenzo Di Marzo
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
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31
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Rocca R, Costa G, Artese A, Parrotta L, Ortuso F, Maccioni E, Pinato O, Greco ML, Sissi C, Alcaro S, Distinto S, Moraca F. Hit Identification of a Novel Dual Binder for h-telo/c-myc G-Quadruplex by a Combination of Pharmacophore Structure-Based Virtual Screening and Docking Refinement. ChemMedChem 2016; 11:1721-33. [PMID: 27008476 DOI: 10.1002/cmdc.201600053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 02/29/2016] [Indexed: 12/28/2022]
Abstract
It is well known that G-quadruplexes are targets of great interest for their roles in crucial biological processes, such as aging and cancer. Hence, a promising strategy for anticancer drug therapy is the stabilization of these structures by small molecules. We report a high-throughput in silico screening of commercial libraries from several different vendors by means of a combined structure-based pharmacophore model approach followed by docking simulations. The compounds selected by the virtual screening procedure were then tested for their ability to interact with human telomeric G-quadruplex folding by circular dichroism, fluorescence spectroscopy, and fluorescence intercalator displacement. Our approach resulted in the identification of a 13-[(dimethylamino)methyl]-12-hydroxy-8H-benzo[c]indolo[3,2,1-ij][1,5]naphthyridin-8-one derivative as a novel promising stabilizer of G-quadruplex structures within the human telomeric and the c-myc promoter sequences.
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Affiliation(s)
- Roberta Rocca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy.
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Elias Maccioni
- Department of Life and Environment Sciences, University of Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Odra Pinato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Maria Laura Greco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Simona Distinto
- Department of Life and Environment Sciences, University of Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
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32
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Foloppe N, Chen IJ. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding. Bioorg Med Chem 2016; 24:2159-89. [PMID: 27061672 DOI: 10.1016/j.bmc.2016.03.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 01/24/2023]
Abstract
There has been an explosion of structural information for pharmaceutical compounds bound to biological targets, but the conformations and dynamics of compounds free in solution are poorly characterized, if at all. Yet, knowledge of the unbound state is essential to understand the fundamentals of molecular recognition, including the much debated conformational intramolecular reorganization energy of a compound upon binding (ΔEReorg). Also, dependable observation of the unbound compounds is important for ligand-based drug discovery, e.g. with pharmacophore modelling. Here, these questions are addressed with long (⩾0.5μs) state-of-the-art molecular dynamics (MD) simulations of 26 compounds (including 7 approved drugs) unbound in explicit solvent. These compounds were selected to be chemically diverse, with a range of flexibility, and good quality bioactive X-ray structures. The MD-simulated free compounds are compared to their bioactive structure and conformers generated with ad hoc sampling in vacuo or with implicit generalized Born (GB) aqueous solvation models. The GB conformational models clearly depart from those obtained in explicit solvent, and suffer from conformational collapse almost as severe as in vacuo. Thus, the global energy minima in vacuo or with GB are not suitable representations of the unbound state, which can instead be extensively sampled by MD simulations. Many, but not all, MD-simulated compounds displayed some structural similarity to their bioactive structure, supporting the notion of conformational pre-organization for binding. The ligand-protein complexes were also simulated in explicit solvent, to estimate ΔEReorg as an enthalpic difference ΔHReorg between the intramolecular energies in the bound and unbound states. This fresh approach yielded ΔHReorg values⩽6kcal/mol for 18 out of 26 compounds. For three particularly polar compounds 15⩽ΔHReorg⩽20kcal/mol, supporting the notion that ΔHReorg can be substantial. Those large ΔHReorg values correspond to a redistribution of electrostatic interactions upon binding. Overall, the study illustrates how MD simulations offer a promising avenue to characterize the unbound state of medicinal compounds.
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Affiliation(s)
- Nicolas Foloppe
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
| | - I-Jen Chen
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, UK.
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33
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Supady A, Blum V, Baldauf C. First-Principles Molecular Structure Search with a Genetic Algorithm. J Chem Inf Model 2015; 55:2338-48. [DOI: 10.1021/acs.jcim.5b00243] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Adriana Supady
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
- Department of Mechanical Engineering & Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
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34
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Kothiwale S, Mendenhall JL, Meiler J. BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library. J Cheminform 2015; 7:47. [PMID: 26473018 PMCID: PMC4607025 DOI: 10.1186/s13321-015-0095-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/03/2015] [Indexed: 12/14/2022] Open
Abstract
The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational space a small molecule can sample is critical for both structure- and ligand-based drug discovery algorithms such as small molecule docking or three-dimensional quantitative structure–activity relationships. Here we have derived a database of small molecule fragments frequently sampled in experimental structures within the Cambridge Structure Database and the Protein Data Bank. Likely conformations of these fragments are stored as ‘rotamers’ in analogy to amino acid side chain rotamer libraries used for rapid sampling of protein conformational space. Explicit fragments take into account correlations between multiple torsion bonds and effect of substituents on torsional profiles. A conformational ensemble for small molecules can then be generated by recombining fragment rotamers with a Monte Carlo search strategy. BCL::Conf was benchmarked against other conformer generator methods including Confgen, Moe, Omega and RDKit in its ability to recover experimentally determined protein bound conformations of small molecules, diversity of conformational ensembles, and sampling rate. BCL::Conf recovers at least one conformation with a root mean square deviation of 2 Å or better to the experimental structure for 99 % of the small molecules in the Vernalis benchmark dataset. The ‘rotamer’ approach will allow integration of BCL::Conf into respective computational biology programs such as Rosetta.Conformation sampling is carried out using explicit fragment conformations derived from crystallographic structure databases. Molecules from the database are decomposed into fragments and most likely conformations/rotamers are used to sample correspondng sub-structure of a molecule of interest. ![]()
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Affiliation(s)
- Sandeepkumar Kothiwale
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232 USA
| | - Jeffrey L Mendenhall
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232 USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232 USA ; Department of Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN 37212 USA
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35
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Fer MJ, Bouhss A, Patrão M, Le Corre L, Pietrancosta N, Amoroso A, Joris B, Mengin-Lecreulx D, Calvet-Vitale S, Gravier-Pelletier C. 5'-Methylene-triazole-substituted-aminoribosyl uridines as MraY inhibitors: synthesis, biological evaluation and molecular modeling. Org Biomol Chem 2015; 13:7193-222. [PMID: 26008868 DOI: 10.1039/c5ob00707k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The straightforward synthesis of 5'-methylene-[1,4]-triazole-substituted aminoribosyl uridines is described. Two families of compounds were synthesized from a unique epoxide which was regioselectively opened by acetylide ions (for compounds II) or azide ions (for compounds III). Sequential diastereoselective glycosylation with a ribosyl fluoride derivative, Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC) with various complementary azide and alkyne partners afforded the targeted compounds after final deprotection. The biological activity of the 16 resulting compounds together with that of 14 previously reported compounds I, lacking the 5' methylene group, was evaluated on the MraY transferase activity. Out of the 30 tested compounds, 18 compounds revealed MraY inhibition with IC50 ranging from 15 to 150 μM. A molecular modeling study was performed to rationalize the observed structure-activity relationships (SAR), which allowed us to correlate the activity of the most potent compounds with an interaction involving Leu191 of MraYAA. The antibacterial activity was also evaluated and seven compounds exhibited a good activity against Gram-positive bacterial pathogens with MIC ranging from 8 to 32 μg mL(-1), including the methicillin resistant Staphylococcus aureus (MRSA).
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Affiliation(s)
- Mickaël J Fer
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, CICB-Paris (Centre Interdisciplinaire Chimie Biologie-Paris), 45 rue des Saints Pères, 75270 Paris 06, France.
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36
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Vuorinen A, Schuster D. Methods for generating and applying pharmacophore models as virtual screening filters and for bioactivity profiling. Methods 2014; 71:113-34. [PMID: 25461773 DOI: 10.1016/j.ymeth.2014.10.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Revised: 09/29/2014] [Accepted: 10/14/2014] [Indexed: 01/03/2023] Open
Abstract
Biological effects of small molecules in an organism result from favorable interactions between the molecules and their target proteins. These interactions depend on chemical functionalities, bonds, and their 3D-orientations towards each other. These 3D-arrangements of chemical functionalities that make a small molecule active towards its target can be described by pharmacophore models. In these models, chemical functionalities are represented as so-called features. Commonly, they are obtained either from a set of active compounds or directly from the observed protein-ligand interactions as present in X-ray crystal structures, NMR structures, or docking poses. In this review, we explain the basics of pharmacophore modeling including dataset generation, 3D-representations and conformational analysis of small molecules, pharmacophore model construction, model validation, and its benefits to virtual screening and other applications.
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Affiliation(s)
- Anna Vuorinen
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck - CMBI, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Daniela Schuster
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck - CMBI, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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37
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Watts KS, Dalal P, Tebben AJ, Cheney DL, Shelley JC. Macrocycle Conformational Sampling with MacroModel. J Chem Inf Model 2014; 54:2680-96. [DOI: 10.1021/ci5001696] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Shawn Watts
- Schrödinger, Inc., 101 SW Main Street,
Suite 1300, Portland, Oregon 97204, United States
| | - Pranav Dalal
- D. E. Shaw India Software, Private Limited, Sanali Infopark, 8-2-120/113, Road No. 2, Banjara
Hills, Hyderabad 500 034, Andhra Pradesh, India
| | - Andrew J. Tebben
- Bristol-Myers Squibb, 3551 Lawrenceville
Road, Princeton, Lawrence Township, New Jersey 08648, United States
| | - Daniel L. Cheney
- Bristol-Myers Squibb, 311 Pennington−Rocky
Hill Road, Pennington, New
Jersey 08543, United States
| | - John C. Shelley
- Schrödinger, Inc., 101 SW Main Street,
Suite 1300, Portland, Oregon 97204, United States
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Fayaz SM, Rajanikant GK. Ensemble pharmacophore meets ensemble docking: a novel screening strategy for the identification of RIPK1 inhibitors. J Comput Aided Mol Des 2014; 28:779-94. [DOI: 10.1007/s10822-014-9771-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/23/2014] [Indexed: 12/29/2022]
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Yadav MK, Singh A, Swati D. A knowledge-based approach for identification of drugs against vivapain-2 protein of Plasmodium vivax through pharmacophore-based virtual screening with comparative modelling. Appl Biochem Biotechnol 2014; 173:2174-88. [PMID: 24970047 DOI: 10.1007/s12010-014-1023-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 06/19/2014] [Indexed: 01/07/2023]
Abstract
Malaria is one of the most infectious diseases in the world. Plasmodium vivax, the pathogen causing endemic malaria in humans worldwide, is responsible for extensive disease morbidity. Due to the emergence of resistance to common anti-malarial drugs, there is a continuous need to develop a new class of drugs for this pathogen. P. vivax cysteine protease, also known as vivapain-2, plays an important role in haemoglobin hydrolysis and is considered essential for the survival of the parasite. The three-dimensional (3D) structure of vivapain-2 is not predicted experimentally, so its structure is modelled by using comparative modelling approach and further validated by Qualitative Model Energy Analysis (QMEAN) and RAMPAGE tools. The potential binding site of selected vivapain-2 structure has been detected by grid-based function prediction method. Drug targets and their respective drugs similar to vivapain-2 have been identified using three publicly available databases: STITCH 3.1, DrugBank and Therapeutic Target Database (TTD). The second approach of this work focuses on docking study of selected drug E-64 against vivapain-2 protein. Docking reveals crucial information about key residues (Asn281, Cys283, Val396 and Asp398) that are responsible for holding the ligand in the active site. The similarity-search criterion is used for the preparation of our in-house database of drugs, obtained from filtering the drugs from the DrugBank database. A five-point 3D pharmacophore model is generated for the docked complex of vivapain-2 with E-64. This study of 3D pharmacophore-based virtual screening results in identifying three new drugs, amongst which one is approved and the other two are experimentally proved. The ADMET properties of these drugs are found to be in the desired range. These drugs with novel scaffolds may act as potent drugs for treating malaria caused by P. vivax.
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Affiliation(s)
- Manoj Kumar Yadav
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi, 221005, India,
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40
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Kumar SP, Jasrai YT, Mehta VP, Pandya HA. Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors. J Biomol Struct Dyn 2014; 33:706-22. [PMID: 24735019 DOI: 10.1080/07391102.2014.908142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantitative pharmacophore hypothesis combines the 3D spatial arrangement of pharmacophore features with biological activities of the ligand data-set and predicts the activities of geometrically and/or pharmacophoric similar ligands. Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands. Towards this focus, we describe a ligand-based computational procedure to introduce flexibility in aligning the small molecules and generating a pharmacophore hypothesis without geometrical constraints to define pharmacophore space, enriched with chemical features necessary to elucidate common pharmacophore hypotheses (CPHs). Maximal common substructure (MCS)-based alignment method was adopted to guide the alignment of carbon molecules, deciphered the MCS atom connectivity to cluster molecules in bins and subsequently, calculated the pharmacophore similarity matrix with the bin-specific reference molecules. After alignment, the carbon molecules were enriched with original atoms in their respective positions and conventional pharmacophore features were perceived. Distance-based pharmacophoric descriptors were enumerated by computing the interdistance between perceived features and MCS-aligned 'centroid' position. The descriptor set and biological activities were used to develop support vector machine models to predict the activities of the external test set. Finally, fitness score was estimated based on pharmacophore similarity with its bin-specific reference molecules to recognize the best and poor alignments and, also with each reference molecule to predict outliers of the quantitative hypothesis model. We applied this procedure to a diverse data-set of 40 HIV-1 integrase inhibitors and discussed its effectiveness with the reported CPH model.
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Affiliation(s)
- Sivakumar Prasanth Kumar
- a Department of Bioinformatics, Applied Botany Centre (ABC) , Gujarat University , Ahmedabad 380009 , Gujarat , India
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41
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Chen IJ, Foloppe N. Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery. Bioorg Med Chem 2013; 21:7898-920. [DOI: 10.1016/j.bmc.2013.10.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 09/29/2013] [Accepted: 10/04/2013] [Indexed: 02/01/2023]
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Yadav MK, Pandey SK, Swati D. DRUG TARGET PRIORITIZATION IN PLASMODIUM FALCIPARUM THROUGH METABOLIC NETWORK ANALYSIS, AND INHIBITOR DESIGNING USING VIRTUAL SCREENING AND DOCKING APPROACH. J Bioinform Comput Biol 2013; 11:1350003. [DOI: 10.1142/s0219720013500030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genome sequence of Plasmodium falciparum reveals that many metabolic pathways are unique as compared to its human host. Metabolic Network Analysis was carried out to find the essential enzymes critical for the survival of the pathogen. In the present study, choke point and load point analysis was used to locate putative targets. The identified targets were further checked to confirm that no alternate pathway or human homolog exists. Among the top 15 enzymes obtained from this analysis, we have selected P. falciparum orotidine-5'-monophosphate decarboxylase (PfODCase) enzyme as it is sequentially and structurally different from that of humans, for searching novel inhibitors. A five-point 3D pharmacophore was generated for the crystal structure of PfODCase complexes with uridine-5'-monophosphate (U5P). The binding site environment shows three H-bond acceptors, one H-bond donor and one negative ionizable feature. This pharmacophore model was used as a 3D query to perform virtual screening experiments against 2,664,779 standard lead compounds obtained from the freely available ZINC database. Top 10 hits obtained from virtual screening were selected for molecular docking experiments against PfODCase in order to verify their results and to have a better insight into their binding modes. Here, docking of U5P with PfODCase is used as a control. We have identified six compounds, among them, few are U5P analogs and others are novel ones with diverse scaffolds. The key residues: Lys42, Asp20, Lys72, Ser127, Ala184, Gln185 and Arg203 at the main binding pocket of PfODCase are responsible for better stability of diverse ligands. These compounds according to their free energy of binding could serve as potent leads for designing novel inhibitors against malarial ODCase enzyme.
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Affiliation(s)
- Manoj Kumar Yadav
- Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi 221005, India.
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43
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State-of-the-art and dissemination of computational tools for drug-design purposes: a survey among Italian academics and industrial institutions. Future Med Chem 2013; 5:907-27. [PMID: 23682568 DOI: 10.4155/fmc.13.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
During the first edition of the Computationally Driven Drug Discovery meeting, held in November 2011 at Dompé Pharma (L'Aquila, Italy), a questionnaire regarding the diffusion and the use of computational tools for drug-design purposes in both academia and industry was distributed among all participants. This is a follow-up of a previously reported investigation carried out among a few companies in 2007. The new questionnaire implemented five sections dedicated to: research group identification and classification; 18 different computational techniques; software information; hardware data; and economical business considerations. In this article, together with a detailed history of the different computational methods, a statistical analysis of the survey results that enabled the identification of the prevalent computational techniques adopted in drug-design projects is reported and a profile of the computational medicinal chemist currently working in academia and pharmaceutical companies in Italy is highlighted.
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44
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Pan Y, Chothe PP, Swaan PW. Identification of novel breast cancer resistance protein (BCRP) inhibitors by virtual screening. Mol Pharm 2013; 10:1236-48. [PMID: 23418667 DOI: 10.1021/mp300547h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Breast cancer resistance protein (BCRP; ABCG2) is an efflux transporter that plays an important role in multidrug resistance to antineoplastic drugs. The identification of drugs as BCRP inhibitors could aid in designing better therapeutic strategies for cancer treatment and will be critical for identifying potential drug-drug interactions. In the present study, we applied ligand-based virtual screening combined with experimental testing for the identification of novel drugs that can possibly interact with BCRP. Bayesian and pharmacophore models generated with known BCRP inhibitors were validated with an external test set. The resulting models were applied to predict new potential drug candidates from a database with more than 2000 FDA-approved drugs. Thirty-three drugs were tested in vitro for their inhibitory effects on BCRP-mediated transport of [(3)H]-mitoxantrone in MCF-7/AdrVp cells. Nineteen drugs were identified with significant inhibitory effect on BCRP transport function. The combined strategy of computational and experimental approaches in this paper has suggested potential drug candidates and thus represents an effective tool for rational identification of modulators of other proteins.
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Affiliation(s)
- Yongmei Pan
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
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45
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Lynch C, Pan Y, Li L, Ferguson SS, Xia M, Swaan PW, Wang H. Identification of novel activators of constitutive androstane receptor from FDA-approved drugs by integrated computational and biological approaches. Pharm Res 2013; 30:489-501. [PMID: 23090669 PMCID: PMC3554869 DOI: 10.1007/s11095-012-0895-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/04/2012] [Indexed: 10/27/2022]
Abstract
PURPOSE The constitutive androstane receptor (CAR, NR1I3) is a xenobiotic sensor governing the transcription of numerous hepatic genes associated with drug metabolism and clearance. Recent evidence suggests that CAR also modulates energy homeostasis and cancer development. Thus, identification of novel human (h) CAR activators is of both clinical importance and scientific interest. METHODS Docking and ligand-based structure-activity models were used for virtual screening of a database containing over 2000 FDA-approved drugs. Identified lead compounds were evaluated in cell-based reporter assays to determine hCAR activation. Potential activators were further tested in human primary hepatocytes (HPHs) for the expression of the prototypical hCAR target gene CYP2B6. RESULTS Nineteen lead compounds with optimal modeling parameters were selected for biological evaluation. Seven of the 19 leads exhibited moderate to potent activation of hCAR. Five out of the seven compounds translocated hCAR from the cytoplasm to the nucleus of HPHs in a concentration-dependent manner. These compounds also induce the expression of CYP2B6 in HPHs with rank-order of efficacies closely resembling that of hCAR activation. CONCLUSION These results indicate that our strategically integrated approaches are effective in the identification of novel hCAR modulators, which may function as valuable research tools or potential therapeutic molecules.
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Affiliation(s)
- Caitlin Lynch
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Yongmei Pan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Linhao Li
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | | | - Menghang Xia
- NIH Chemical Genomics Center, National Institutes of Health, Bethesda, Maryland 20892
| | - Peter W. Swaan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201
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Kraft P, Denizot N. Synthesis of a Spirocyclic Seco Structure of the Principal Vetiver Odorant Khusimone. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201318] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hawkins PCD, Nicholls A. Conformer generation with OMEGA: learning from the data set and the analysis of failures. J Chem Inf Model 2012; 52:2919-36. [PMID: 23082786 DOI: 10.1021/ci300314k] [Citation(s) in RCA: 308] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We recently published a high quality validation set for testing conformer generators, consisting of structures from both the PDB and the CSD (Hawkins, P. C. D. et al. J. Chem. Inf. Model. 2010, 50, 572.), and tested the performance of our conformer generator, OMEGA, on these sets. In the present publication, we focus on understanding the suitability of those data sets for validation and identifying and learning from OMEGA's failures. We compare, for the first time we are aware of, the coverage of the applicable property spaces between the validation data sets we used and the parent compound sets to determine if our data sets adequately sample these property spaces. We also introduce the concept of torsion fingerprinting and compare this method of dissimilation to the more traditional graph-centric diversification methods we used in our previous publication. To improve our ability to programmatically identify cases where the crystallographic conformation is not well reproduced computationally, we introduce a new metric to compare conformations, RMSTanimoto. This new metric is used alongside those from our previous publication to efficiently identify reproduction failures. We find RMSTanimoto to be particularly effective in identifying failures for the smallest molecules in our data sets. Analysis of the nature of these failures, particularly those for the CSD, sheds further light on the issue of strain in crystallographic structures. Some of the residual failure cases not resolved by simple changes in OMEGA's defaults present significant challenges to conformer generation engines like OMEGA and are a source of new avenues to further improve their performance, while others illustrate the pitfalls of validating against crystallographic ligand conformations, particularly those from the PDB.
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Affiliation(s)
- Paul C D Hawkins
- OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, USA.
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Musafia B, Senderowitz H. Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design. Expert Opin Drug Discov 2012; 5:943-59. [PMID: 22823989 DOI: 10.1517/17460441.2010.513711] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD In silico or virtual screening has become a common practice in contemporary computer-aided drug discovery efforts and currently constitutes a reasonably mature paradigm. Application of ligand-based approaches to virtual screening requires the ability to identify the bioactive conformers of drug-like compounds as these conformers are expected to elicit the biological activity. However, given the complexity of the energy potential surfaces of such ligands and in particular those exhibiting some degree of flexibility and the limitation of contemporary energy functions, this is not an easy task. AREAS COVERED IN THIS REVIEW The current contribution provides an in-depth review of recent developments in the field of generating conformational ensembles of drug-like compounds with a particular emphasis of focusing such ensembles on bioactive conformers using both energy and structural criteria. The literature reviewed in this manuscript roughly covers the last decade. WHAT THE READER WILL GAIN Readers of this review will gain an appreciation for the complexity of identifying bioactive conformers of drug-like compounds and an exposure to the different computational methods which were developed in order to tackle this problem as well as to the remaining challenges in this field. TAKE HOME MESSAGE The identification of ensembles of bioactive conformers of drug-like compounds is far from being a solved problem. Recent research has advanced the field to the point where bioactive conformers could be readily identified from within conformational ensembles generated by contemporary computational tools. However, as such conformers are inevitably accompanied by many other non-relevant conformations, a focusing mechanism is required. New methods in this field are showing promise but more work is clearly needed. New research lines are proposed which are believed to enhance the performances and with it the usefulness of 3D ligand-based methods in drug discovery and development.
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Leng Y, Lu T, Yuan HL, Liu HC, Lu S, Zhang WW, Jiang YL, Chen YD. QSAR studies on imidazopyrazine derivatives as Aurora A kinase inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:705-730. [PMID: 22971111 DOI: 10.1080/1062936x.2012.719541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Aurora kinases have emerged as attractive targets for the development of novel anti-cancer agents. A combined study of molecular docking, pharmacophore modelling and 3D-QSAR was performed on a series of imidazo [1, 2-a] pyrazines as novel Aurora kinase inhibitors to gain insights into the structural determinants and their structure-activity relationship. An ensemble of conformations based on molecular docking was used for PHASE pharmacophore studies. The developed best-fitted pharmacophore model was validated by diverse chemotypes of Aurora A kinase inhibitors and was consistent with the structural requirements for the docked binding mechanism. Subsequently, the pharmacophore-based alignment was used to develop PHASE and comparative molecular similarity indices analysis (CoMSIA) 3D-QSAR models. The best CoMSIA model showed good statistics (q (2 )= 0.567, r (2 )= 0.992), and the predictive ability of the model was validated using an external test set of 13 compounds giving a satisfactory prediction ([Formula: see text]). The 3D contour maps provided insight into the binding mechanism and highlighted key structural features that are essential to the inhibitory activity. Based on the PHASE and CoMSIA 3D-QSAR results, a set of novel Aurora A inhibitors were designed that showed excellent potencies.
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Affiliation(s)
- Y Leng
- Laboratory of Molecular Design and Drug Discovery, School of Basic Science, China Pharmaceutical University, Nanjing, China
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50
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Handzlik J, Szymańska E, Wójcik R, Dela A, Jastrzębska-Więsek M, Karolak-Wojciechowska J, Fruziński A, Siwek A, Filipek B, Kieć-Kononowicz K. Synthesis and SAR-study for novel arylpiperazine derivatives of 5-arylidenehydantoin with α1-adrenoceptor antagonistic properties. Bioorg Med Chem 2012; 20:4245-57. [DOI: 10.1016/j.bmc.2012.05.064] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 05/21/2012] [Accepted: 05/25/2012] [Indexed: 11/25/2022]
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