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Assessing How Residual Errors of Scoring Functions Correlate to Ligand Structural Features. Int J Mol Sci 2022; 23:ijms232315018. [PMID: 36499344 PMCID: PMC9739603 DOI: 10.3390/ijms232315018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Scoring functions (SFs) are ubiquitous tools for early stage drug discovery. However, their accuracy currently remains quite moderate. Despite a number of successful target-specific SFs appearing recently, up until now, no ideas on how to systematically improve the general scope of SFs have been formulated. In this work, we hypothesized that the specific features of ligands, corresponding to interactions well appreciated by medicinal chemists (e.g., hydrogen bonds, hydrophobic and aromatic interactions), might be responsible, in part, for the remaining SF errors. The latter provides direction to efforts aimed at the rational and systematic improvement of SF accuracy. In this proof-of-concept work, we took a CASF-2016 coreset of 285 ligands as a basis for comparison and calculated the values of scores for a representative panel of SFs (including AutoDock 4.2, AutoDock Vina, X-Score, NNScore2.0, ΔVina RF20, and DSX). The residual error of linear correlation of each SF value, with the experimental values of affinity and activity, was then analyzed in terms of its correlation with the presence of the fragments responsible for certain medicinal chemistry defined interactions. We showed that, despite the fact that SFs generally perform reasonably, there is room for improvement in terms of better parameterization of interactions involving certain fragments in ligands. Thus, this approach opens a potential way for the systematic improvement of SFs without their significant complication. However, the straightforward application of the proposed approach is limited by the scarcity of reliable available data for ligand-receptor complexes, which is a common problem in the field.
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Nadal-Gratacós N, Lleixà E, Gibert-Serramià M, Estrada-Tejedor R, Berzosa X, Batllori X, Pubill D, Camarasa J, Escubedo E, López-Arnau R. Neuropsychopharmacology of Emerging Drugs of Abuse: meta- and para-Halogen-Ring-Substituted α-PVP (“flakka”) Derivatives. Int J Mol Sci 2022; 23:ijms23042226. [PMID: 35216339 PMCID: PMC8876800 DOI: 10.3390/ijms23042226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
Changes in the molecular structure of synthetic cathinones has led to an increase in the number of novel emerging drugs in the illicit drug market at an unprecedented rate. Unfortunately, little is known about the neuropsychopharmacology of recently emerged halogen-substituted α-PVP derivatives. Thus, the aim of this study was to investigate the role of para- and meta-halogen (F-, Cl-, and Br-) substitutions on the in vitro, in silico, and in vivo effects of α-pyrrolidinopentiophenone (α-PVP) derivatives. HEK293 cells expressing the human dopamine or serotonin transporter (hDAT and hSERT) were used for the uptake inhibition and transporter affinity assays. Molecular docking was used to model the interaction mechanism against DAT. Swiss CD-1 mice were used for the horizontal locomotor activity, open field test, and conditioned place preference paradigm. All compounds demonstrated potent DA uptake inhibition and higher DAT selectivity than cocaine. Meta-substituted cathinones showed higher DAT/SERT ratios than their para- analogs, which correlates with an increased psychostimulant effect in vivo and with different meta- and para-in silico interactions at DAT. Moreover, all compounds induced rewarding and acute anxiogenic effects in mice. In conclusion, the present study demonstrates the role of meta- and para-halogen substitutions in the mechanism of action and provides the first evidence of the rewarding and anxiety-like properties of halogenated α-PVP derivatives.
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Affiliation(s)
- Núria Nadal-Gratacós
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Institute of Biomedicine (IBUB), Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain; (N.N.-G.); (E.L.); (M.G.-S.); (D.P.); (J.C.)
- Pharmaceutical Chemistry Group (GQF), IQS School of Engineering, Universitat Ramon Llull, 08017 Barcelona, Spain; (R.E.-T.); (X.B.); (X.B.)
| | - Esther Lleixà
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Institute of Biomedicine (IBUB), Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain; (N.N.-G.); (E.L.); (M.G.-S.); (D.P.); (J.C.)
- Pharmaceutical Chemistry Group (GQF), IQS School of Engineering, Universitat Ramon Llull, 08017 Barcelona, Spain; (R.E.-T.); (X.B.); (X.B.)
| | - Mónica Gibert-Serramià
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Institute of Biomedicine (IBUB), Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain; (N.N.-G.); (E.L.); (M.G.-S.); (D.P.); (J.C.)
| | - Roger Estrada-Tejedor
- Pharmaceutical Chemistry Group (GQF), IQS School of Engineering, Universitat Ramon Llull, 08017 Barcelona, Spain; (R.E.-T.); (X.B.); (X.B.)
| | - Xavier Berzosa
- Pharmaceutical Chemistry Group (GQF), IQS School of Engineering, Universitat Ramon Llull, 08017 Barcelona, Spain; (R.E.-T.); (X.B.); (X.B.)
| | - Xavier Batllori
- Pharmaceutical Chemistry Group (GQF), IQS School of Engineering, Universitat Ramon Llull, 08017 Barcelona, Spain; (R.E.-T.); (X.B.); (X.B.)
| | - David Pubill
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Institute of Biomedicine (IBUB), Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain; (N.N.-G.); (E.L.); (M.G.-S.); (D.P.); (J.C.)
| | - Jordi Camarasa
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Institute of Biomedicine (IBUB), Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain; (N.N.-G.); (E.L.); (M.G.-S.); (D.P.); (J.C.)
| | - Elena Escubedo
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Institute of Biomedicine (IBUB), Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain; (N.N.-G.); (E.L.); (M.G.-S.); (D.P.); (J.C.)
- Correspondence: (E.E.); (R.L.-A.); Tel.: +34-9-3402-4531 (E.E.)
| | - Raúl López-Arnau
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, Institute of Biomedicine (IBUB), Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain; (N.N.-G.); (E.L.); (M.G.-S.); (D.P.); (J.C.)
- Correspondence: (E.E.); (R.L.-A.); Tel.: +34-9-3402-4531 (E.E.)
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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Anisotropic electrostatic models of nitrogen and phosphorus: the variation and the interpretability of the electrostatic parameters in response to structure variation. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Costa PJ, Nunes R, Vila-Viçosa D. Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design. Expert Opin Drug Discov 2019; 14:805-820. [PMID: 31131651 DOI: 10.1080/17460441.2019.1619692] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.
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Affiliation(s)
- Paulo J Costa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Rafael Nunes
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Diogo Vila-Viçosa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
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Titov OI, Shulga DA, Palyulin VA. Quadrupole Correction: From Molecular Electrostatic Potential to Free Energies of Halogen Bonding. J Chem Theory Comput 2018; 15:1159-1167. [DOI: 10.1021/acs.jctc.8b00739] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Oleg I. Titov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A. Shulga
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vladimir A. Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
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Shulga DA, Titov OI, Pisarev SA, Palyulin VA. Multipole models of sulphur for accurate anisotropic electrostatic interactions within force fields. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:21-42. [PMID: 29254381 DOI: 10.1080/1062936x.2017.1406403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Nowadays, as computing has become much more available, a fresh momentum has been observed in the field of re-visioning and re-parameterizing the usual tools, as well as estimating for the incorporation of new qualitative capabilities, aimed at making more accurate and reliable predictions in drug discovery processes. Inspired by the success of modelling the electrostatic part of the halogen bonding (XB) by means of the distributed multipole expansion, a study is presented which attempts to extend this approach to a tougher case of σ-hole interaction: sulphur-based chalcogen bonding. To that end, 11 anisotropic models have been derived and tested for their performance in the reproduction of reference ab initio molecular electrostatic potential. A careful examination resulted in three models which have been selected for further examination as a part of the molecular mechanics force field (GAFF). The combined force field was used to estimate inter- and intra-molecular interactions for the molecular systems, capable of differentiating the binding from the σ-hole and other directions. The anisotropic models proposed were generally able to correct the wrong predictions of the sulphur models based only on isotropic charges and, thus, are a promising direction for further development of the refined electrostatics force fields.
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Affiliation(s)
- D A Shulga
- a Department of Chemistry , Lomonosov Moscow State University , Moscow , Russia
| | - O I Titov
- a Department of Chemistry , Lomonosov Moscow State University , Moscow , Russia
| | - S A Pisarev
- b Institute of Physiologically Active Compounds , Russian Academy of Sciences , Chernogolovka , Russia
| | - V A Palyulin
- a Department of Chemistry , Lomonosov Moscow State University , Moscow , Russia
- b Institute of Physiologically Active Compounds , Russian Academy of Sciences , Chernogolovka , Russia
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Titov OI, Shulga DA, Palyulin VA, Zefirov NS. Quadrupole correction for halogen bonding description in virtual screening and molecular docking. DOKLADY CHEMISTRY 2016. [DOI: 10.1134/s0012500816110100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Li Y, Guo B, Xu Z, Li B, Cai T, Zhang X, Yu Y, Wang H, Shi J, Zhu W. Repositioning organohalogen drugs: a case study for identification of potent B-Raf V600E inhibitors via docking and bioassay. Sci Rep 2016; 6:31074. [PMID: 27501852 PMCID: PMC4977465 DOI: 10.1038/srep31074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/14/2016] [Indexed: 11/09/2022] Open
Abstract
Drug repositioning has been attracting increasingly attention for its advantages of reducing costs and risks. Statistics showed that around one quarter of the marketed drugs are organohalogens. However, no study has been reported, to the best of our knowledge, to aim at efficiently repositioning organohalogen drugs, which may be attributed to the lack of accurate halogen bonding scoring function. Here, we present a study to show that two organohalogen drugs were successfully repositioned as potent B-Raf V600E inhibitors via molecular docking with halogen bonding scoring function, namely D(3)DOCKxb developed in our lab, and bioassay. After virtual screening by D(3)DOCKxb against the database CMC (Comprehensive Medicinal Chemistry), 3 organohalogen drugs that were predicted to form strong halogen bonding with B-Raf V600E were purchased and tested with ELISA-based assay. In the end, 2 of them, rafoxanide and closantel, were identified as potent inhibitors with IC50 values of 0.07 μM and 1.90 μM, respectively, which are comparable to that of vemurafenib (IC50: 0.17 μM), a marketed drug targeting B-Raf V600E. Single point mutagenesis experiments confirmed the conformations predicted by D(3)DOCKxb. And comparison experiment revealed that halogen bonding scoring function is essential for repositioning those drugs with heavy halogen atoms in their molecular structures.
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Affiliation(s)
- Yisu Li
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, Jiangsu, 215123, China
| | - Binbin Guo
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bo Li
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Tingting Cai
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xinben Zhang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yuqi Yu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Heyao Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiye Shi
- UCB Biopharma SPRL, Chemin du Foriest, Braine-l’Alleud, Belgium
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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Affiliation(s)
- Michal H. Kolář
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute
of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations
(IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Federal Republic of Germany
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacky University, 771 46 Olomouc, Czech Republic
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Adasme-Carreño F, Muñoz-Gutierrez C, Alzate-Morales JH. Halogen bonding in drug-like molecules: a computational and systematic study of the substituent effect. RSC Adv 2016. [DOI: 10.1039/c6ra14837a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Systematic study of the effect of fourteen chemical groups at the ortho, para and meta positions of NMA⋯halobenzene complexes showed a significant influence on halogen bonding, and also non-additive effects. A comprehensive description is reported.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
| | - Camila Muñoz-Gutierrez
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
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