1
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Szél V, Zsidó BZ, Jeszenői N, Hetényi C. Target-ligand binding affinity from single point enthalpy calculation and elemental composition. Phys Chem Chem Phys 2023; 25:31714-31725. [PMID: 37964670 DOI: 10.1039/d3cp04483a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Reliable target-ligand binding thermodynamics data are essential for successful drug design and molecular engineering projects. Besides experimental methods, a number of theoretical approaches have been introduced for the generation of binding thermodynamics data. However, available approaches often neglect electronic effects or explicit water molecules influencing target-ligand interactions. To handle electronic effects within a reasonable time frame, we introduce a fast calculator QMH-L using a single target-ligand complex structure pre-optimized at the molecular mechanics level. QMH-L is composed of the semi-empirical quantum mechanics calculation of binding enthalpy with predicted explicit water molecules at the complex interface, and a simple descriptor based on the elemental composition of the ligand. QMH-L estimates the target-ligand binding free energy with a root mean square error (RMSE) of 0.94 kcal mol-1. The calculations also provide binding enthalpy values and they were compared with experimental binding thermodynamics data collected from the most reliable isothermal titration calorimetry studies of systems including various protein targets and challenging, large peptide ligands with a molecular weight of up to 2-3 thousand. The single point enthalpy calculations of QMH-L require modest computational resources and are based on short runs with open source and/or free software like Gromacs, Mopac, MobyWat, and Fragmenter. QMH-L can be applied for fast, automated scoring of drug candidates during a virtual screen, enthalpic engineering of new ligands or thermodynamic explanation of complex interactions.
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Affiliation(s)
- Viktor Szél
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Norbert Jeszenői
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary.
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2
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Melse O, Antes I, Kaila VRI, Zacharias M. Benchmarking biomolecular force field-based Zn 2+ for mono- and bimetallic ligand binding sites. J Comput Chem 2023; 44:912-926. [PMID: 36495007 DOI: 10.1002/jcc.27052] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Zn2+ is one of the most versatile biologically available metal ions, but accurate modeling of Zn2+ -containing metalloproteins at the biomolecular force field level can be challenging. Since most Zn2+ models are parameterized in bulk solvent, in-depth knowledge about their performance in a protein environment is limited. Thus, we systematically investigate here the behavior of non-polarizable Zn2+ models for their ability to reproduce experimentally determined metal coordination and ligand binding in metalloproteins. The benchmarking is performed in challenging environments, including mono- (carbonic anhydrase II) and bimetallic (metallo-β-lactamase VIM-2) ligand binding sites. We identify key differences in the performance between the Zn2+ models with regard to the preferred ligating atoms (charged/non-charged), attraction of water molecules, and the preferred coordination geometry. Based on these results, we suggest suitable simulation conditions for varying Zn2+ site geometries that could guide the further development of biomolecular Zn2+ models.
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Affiliation(s)
- Okke Melse
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.,SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Iris Antes
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.,SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany
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3
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Duran HE. Pyrimidines: Molecular docking and inhibition studies on carbonic anhydrase and cholinesterases. Biotechnol Appl Biochem 2023; 70:68-82. [PMID: 35112394 DOI: 10.1002/bab.2329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/18/2022] [Indexed: 11/12/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder. The disease is characterized by dementia, memory impairment, cognitive impairment, and speech impairment. Cholinesterases (ChEs; AChE, acetylcholinesterase and BChE, butyrylcholinesterase) inhibitors and their benefits of cholinergic replacement in the treatment of AD have been researched and documented by scientists in various ways to date. Recent studies prove that human carbonic anhydrases (hCAs) are also one of the important targets in the treatment of AD. Therefore, the development of new agents that can simultaneously modulate the various mechanisms or targets involved in the AD pathway may be a powerful strategy to treat AD, the current disease. Considering these data, the effects of the pyrimidines (1-7) were investigated in this study for the discovery and development of multitargeted ChEs and hCAs inhibitors associated with AD. In addition, the molecular docking analysis of the 4-amino-2-choloropyrimidine (2) was performed to understand the binding interactions on the active site of the enzyme. All compounds (1-7) showed satisfactory enzyme inhibitory potency in micromolar concentrations against AChE, BChE, hCAI, and hCAII with KI values ranging from 0.099 to 0.241 μM, from 1.324 to 3.418 μM, from 0.201 to 0.884 μM, from 1.867 to 3.913 μM, respectively. Due to their ChEs and hCAs inhibition, these compounds (1-7) may be considered as leads for investigations in neurodegenerative diseases. All these results revealed that the 4-amino-5,6-dichloropyrimidine (7) (KI value of 0.201 ± 0.041 μM for hCA I), the 4-amino-6-hydroxypyrimidine (4) (KI value of 1.867 ± 0.296 μM for hCA II), the 4-amino-5,6-dichloropyrimidine (7) (KI value of 0.099 ± 0.008 μM for AChE), and the 4-amino-2-chloropyrimidine (2) (KI value of 1.324 ± 0.273 μM for BChE) from the pyrimidines in this series were the most promising derivatives, as they exhibited a good multifunctional inhibition at all experimental levels and in the in silico validation against these enzymes, for the treatment of AD.
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Affiliation(s)
- Hatice Esra Duran
- Department of Medical Biochemistry, Faculty of Medicine, Kafkas University, Kars, Turkey
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4
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Řezáč J, Stewart JJP. How well do semiempirical QM methods describe the structure of proteins? J Chem Phys 2023; 158:044118. [PMID: 36725526 DOI: 10.1063/5.0135091] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Semiempirical quantum-mechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: the ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6-D3H4, PM7, and GFN2-xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6-D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.
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Affiliation(s)
- J Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16000 Prague, Czech Republic
| | - J J P Stewart
- Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, Colorado 80921, USA
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5
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Hameedi MA, T Prates E, Garvin MR, Mathews II, Amos BK, Demerdash O, Bechthold M, Iyer M, Rahighi S, Kneller DW, Kovalevsky A, Irle S, Vuong VQ, Mitchell JC, Labbe A, Galanie S, Wakatsuki S, Jacobson D. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nat Commun 2022; 13:5285. [PMID: 36075915 PMCID: PMC9453703 DOI: 10.1038/s41467-022-32922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 08/23/2022] [Indexed: 11/15/2022] Open
Abstract
In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO226-234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.
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Affiliation(s)
- Mikhail A Hameedi
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Biosciences, Menlo Park, CA, 94025, USA
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Erica T Prates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael R Garvin
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Irimpan I Mathews
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA
| | - B Kirtley Amos
- Department of Horticulture, University of Kentucky, Lexington, KY, USA
| | - Omar Demerdash
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mark Bechthold
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA
| | - Mamta Iyer
- Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Simin Rahighi
- Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Daniel W Kneller
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Andrey Kovalevsky
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Stephan Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Van-Quan Vuong
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Julie C Mitchell
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Audrey Labbe
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Soichi Wakatsuki
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA.
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Biosciences, Menlo Park, CA, 94025, USA.
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA.
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
| | - Daniel Jacobson
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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6
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Güleç Ö, Türkeş C, Arslan M, Demir Y, Yeni Y, Hacımüftüoğlu A, Ereminsoy E, Küfrevioğlu Öİ, Beydemir Ş. Cytotoxic effect, enzyme inhibition, and in silico studies of some novel N-substituted sulfonyl amides incorporating 1,3,4-oxadiazol structural motif. Mol Divers 2022; 26:2825-2845. [PMID: 35397086 PMCID: PMC8994094 DOI: 10.1007/s11030-022-10422-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/21/2022] [Indexed: 12/14/2022]
Abstract
Abstract The acetylcholinesterase and carbonic anhydrase inhibitors (AChEIs and hCAIs) remain key therapeutic agents for many bioactivities such as anti-Alzheimer and antiobesity antiepileptic, anticancer, antiinfective, antiglaucoma, and diuretic effects. Here, it has been attempted to discover novel multi-target AChEIs and hCAIs that are highly potent, orally bioavailable, may be brain penetrant, and have higher effectiveness at lower doses than tacrine and acetazolamide. After detailed investigations both in vitro and in silico, novel N-substituted sulfonyl amide derivatives (6a–j) were determined to be highly potent inhibitors for AChE and hCAs (KIs are in the range of 23.11–52.49 nM, 18.66–59.62 nM, and 9.33–120.80 nM for AChE, hCA I, and hCA II, respectively). Moreover, according to the cytotoxic effect studies, such as the ADME-Tox, cortex neuron cells, and neuroblastoma SH-SY5Y cell line, compounds 6a, 6d, and 6h, which are the most potent representative versus the target enzymes, were identified as orally bioavailable, highly selective, and brain preferentially distributed AChEIs and hCAIs. The docking studies revealed precise binding modes between 6a, 6d, and 6h and hCA II, hCA I, and AChE, respectively. The results presented here might provide a solid basis for further investigation into more potent AChEIs and hCAIs. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11030-022-10422-8.
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Affiliation(s)
- Özcan Güleç
- Department of Chemistry, Faculty of Arts and Science, Sakarya University, 54187, Serdivan, Sakarya, Türkiye
| | - Cüneyt Türkeş
- Department of Biochemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, 24002, Erzincan, Türkiye.
| | - Mustafa Arslan
- Department of Chemistry, Faculty of Arts and Science, Sakarya University, 54187, Serdivan, Sakarya, Türkiye.
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, 75700, Ardahan, Türkiye
| | - Yeşim Yeni
- Department of Medical Pharmacology, Faculty of Medicine, Atatürk University, 25240, Erzurum, Türkiye
| | - Ahmet Hacımüftüoğlu
- Department of Medical Pharmacology, Faculty of Medicine, Atatürk University, 25240, Erzurum, Türkiye
| | - Ergün Ereminsoy
- Department of Chemistry, Faculty of Science, Atatürk University, 25240, Erzurum, Türkiye
| | - Ömer İrfan Küfrevioğlu
- Department of Chemistry, Faculty of Science, Atatürk University, 25240, Erzurum, Türkiye
| | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470, Eskişehir, Türkiye.,The Rectorate of Bilecik Şeyh Edebali University, 11230, Bilecik, Türkiye
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7
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Gnanasekaran R, Xu Y. Understanding the Energetic Components Influencing the Thermodynamic Quantities of Carbonic Anhydrase Protein upon Ligand Binding. ChemistrySelect 2022. [DOI: 10.1002/slct.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Yao Xu
- Warshel Institute for Computational Biology School of Life and Health Sciences The Chinese University of Hong Kong (Shenzhen) Shenzhen 518172 P. R. China
- School of Life Science University of Science and Technology of China Hefei 230026 P. R. China
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8
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Qu X, Dong L, Si Y, Zhao Y, Wang Q, Su P, Wang B. Reliable Prediction of the Protein-Ligand Binding Affinity Using a Charge Penetration Corrected AMOEBA Force Field: A Case Study of Drug Resistance Mutations in Abl Kinase. J Chem Theory Comput 2022; 18:1692-1700. [PMID: 35107298 DOI: 10.1021/acs.jctc.1c01005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein mutations that directly impair drug binding are related to therapeutic resistance, and accurate prediction of their impact on drug binding would benefit drug design and clinical practice. Here, we have developed a scoring strategy that predicts the effect of the mutations on the protein-ligand binding affinity. In view of the critical importance of electrostatics in protein-ligand interactions, the charge penetration corrected AMOEBA force field (AMOEBA_CP model) was employed to improve the accuracy of the calculated electrostatic energy. We calculated the electrostatic energy using an energy decomposition analysis scheme based on the generalized Kohn-Sham (GKS-EDA). The AMOEBA_CP model was validated by a protein-fragment-ligand complex data set (Abl236) constructed from the co-crystal structures of the cancer target Abl kinase with six inhibitors. To predict ligand binding affinity changes upon protein mutation of Abl kinase, we used sampling protocol with multistep simulated annealing to search conformations of mutant proteins. The scoring strategy based on AMOEBA_CP model has achieved considerable performance in predicting resistance for 8 kinase inhibitors across 144 clinically identified point mutations. Overall, this study illustrates that the AMOEBA_CP model, which accurately treats electrostatics through penetration correction, enables the accurate prediction of the mutation-induced variation of protein-ligand binding affinity.
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Affiliation(s)
- Xiaoyang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Lina Dong
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yubing Si
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, P. R. China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Peifeng Su
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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9
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Smola M, Gutten O, Dejmek M, Kožíšek M, Evangelidis T, Tehrani ZA, Novotná B, Nencka R, Birkuš G, Rulíšek L, Boura E. Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein. Angew Chem Int Ed Engl 2021; 60:10172-10178. [PMID: 33616279 PMCID: PMC8251555 DOI: 10.1002/anie.202016805] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/19/2022]
Abstract
STING (stimulator of interferon genes) is a key regulator of innate immunity that has recently been recognized as a promising drug target. STING is activated by cyclic dinucleotides (CDNs) which eventually leads to expression of type I interferons and other cytokines. Factors underlying the affinity of various CDN analogues are poorly understood. Herein, we correlate structural biology, isothermal calorimetry (ITC) and computational modeling to elucidate factors contributing to binding of six CDNs-three pairs of natural (ribo) and fluorinated (2'-fluororibo) 3',3'-CDNs. X-ray structural analyses of six {STING:CDN} complexes did not offer any explanation for the different affinities of the studied ligands. ITC showed entropy/enthalpy compensation up to 25 kcal mol-1 for this set of similar ligands. The higher affinities of fluorinated analogues are explained with help of computational methods by smaller loss of entropy upon binding and by smaller strain (free) energy.
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Affiliation(s)
- Miroslav Smola
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Ondrej Gutten
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Milan Dejmek
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Milan Kožíšek
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Thomas Evangelidis
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Zahra Aliakbar Tehrani
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Barbora Novotná
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Radim Nencka
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Gabriel Birkuš
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Lubomír Rulíšek
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Evzen Boura
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
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10
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Rocha-Santos A, Chaves EJ, Grillo IB, de Freitas AS, Araújo DAM, Rocha GB. Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors. ACS OMEGA 2021; 6:8764-8777. [PMID: 33842748 PMCID: PMC8027999 DOI: 10.1021/acsomega.0c02588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/30/2020] [Indexed: 05/03/2023]
Abstract
In this work, we performed a study to assess the interactions between the ricin toxin A (RTA) subunit of ricin and some of its inhibitors using modern semiempirical quantum chemistry and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods. Two approaches were followed (calculation of binding enthalpies, ΔH bind, and reactivity quantum chemical descriptors) and compared with the respective half-maximal inhibitory concentration (IC50) experimental data, to gain insight into RTA inhibitors and verify which quantum chemical method would better describe RTA-ligand interactions. The geometries for all RTA-ligand complexes were obtained after running classical molecular dynamics simulations in aqueous media. We found that single-point energy calculations of ΔH bind with the PM6-DH+, PM6-D3H4, and PM7 semiempirical methods and ONIOM QM/MM presented a good correlation with the IC50 data. We also observed, however, that the correlation decreased significantly when we calculated ΔH bind after full-atom geometry optimization with all semiempirical methods. Based on the results from reactivity descriptors calculations for the cases studied, we noted that both types of interactions, molecular overlap and electrostatic interactions, play significant roles in the overall affinity of these ligands for the RTA binding pocket.
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Affiliation(s)
- Acassio Rocha-Santos
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Elton José
Ferreira Chaves
- Department
of Biotechnology, Federal University of
Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Igor Barden Grillo
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | - Amanara Souza de Freitas
- Department
of Chemical Engineering, Federal University
of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
| | | | - Gerd Bruno Rocha
- Department
of Chemistry, Federal University of Paraíba, Cidade Universitária, João Pessoa, PB 58051-900, Brazil
- . Phone/Fax: +55-83-3216-7437
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11
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Smola M, Gutten O, Dejmek M, Kožíšek M, Evangelidis T, Tehrani ZA, Novotná B, Nencka R, Birkuš G, Rulíšek L, Boura E. Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miroslav Smola
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Ondrej Gutten
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Milan Dejmek
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Milan Kožíšek
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Thomas Evangelidis
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Zahra Aliakbar Tehrani
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Barbora Novotná
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Radim Nencka
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Gabriel Birkuš
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Lubomír Rulíšek
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Evzen Boura
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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12
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D’Ambrosio K, Di Fiore A, Buonanno M, Kumari S, Tiwari M, Supuran CT, Mishra CB, Monti SM, De Simone G. The crystal structures of 2-(4-benzhydrylpiperazin-1-yl)- N-(4-sulfamoylphenyl)acetamide in complex with human carbonic anhydrase II and VII provide insights into selective CA inhibitor development. NEW J CHEM 2021. [DOI: 10.1039/d0nj03544k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Our studies suggest that the acetamide linker and long tails are suitable structural features to design selective CA inhibitors.
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Affiliation(s)
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR
- Napoli
- Italy
| | | | - Shikha Kumari
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi
- India
| | - Manisha Tiwari
- Dr. B. R. Ambedkar Centre for Biomedical Research
- University of Delhi
- Delhi
- India
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13
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2362-2371. [PMID: 32609421 DOI: 10.1002/cplu.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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14
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Cavasotto CN, Aucar MG. High-Throughput Docking Using Quantum Mechanical Scoring. Front Chem 2020; 8:246. [PMID: 32373579 PMCID: PMC7186494 DOI: 10.3389/fchem.2020.00246] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/16/2020] [Indexed: 11/13/2022] Open
Abstract
Today high-throughput docking is one of the most commonly used computational tools in drug lead discovery. While there has been an impressive methodological improvement in docking accuracy, docking scoring still remains an open challenge. Most docking programs are rooted in classical molecular mechanics. However, to better characterize protein-ligand interactions, the use of a more accurate quantum mechanical (QM) description would be necessary. In this work, we introduce a QM-based docking scoring function for high-throughput docking and evaluate it on 10 protein systems belonging to diverse protein families, and with different binding site characteristics. Outstanding results were obtained, with our QM scoring function displaying much higher enrichment (screening power) than a traditional docking method. It is acknowledged that developments in quantum mechanics theory, algorithms and computer hardware throughout the upcoming years will allow semi-empirical (or low-cost) quantum mechanical methods to slowly replace force-field calculations. It is thus urgently needed to develop and validate novel quantum mechanical-based scoring functions for high-throughput docking toward more accurate methods for the identification and optimization of modulators of pharmaceutically relevant targets.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Argentina
| | - M Gabriela Aucar
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Argentina
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15
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Optimization of norbornyl‐based carbocyclic nucleoside analogs as cyclin‐dependent kinase 2 inhibitors. J Mol Recognit 2020; 33:e2842. [DOI: 10.1002/jmr.2842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/26/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
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16
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Kříž K, Řezáč J. Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design. J Chem Inf Model 2020; 60:1453-1460. [PMID: 32062970 DOI: 10.1021/acs.jcim.9b01171] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The semiempirical quantum mechanical (SQM) methods used in drug design are commonly parametrized and tested on data sets of systems that may not be representative models for drug-biomolecule interactions in terms of both size and chemical composition. This is addressed here with a new benchmark data set, PLF547, derived from protein-ligand complexes, consisting of complexes of ligands with protein fragments (such as amino-acid side chains), with interaction energies based on MP2-F12 and DLPNO-CCSD(T) calculations. From these, composite benchmark interaction energies are also built for complexes of the ligand with the complete active site of the protein (PLA15 data set). These data sets are used to test multiple SQM methods with corrections for noncovalent interactions; the role of the solvation model in the calculations is tested as well.
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Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Praha 2, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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17
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Olgac A, Yalcin I, Aki-Yalcin E. The 12 th AFMC International Medicinal Chemistry Symposium (AIMECS 2019) in Istanbul, Turkey. ChemMedChem 2020; 15:162-167. [PMID: 31724830 DOI: 10.1002/cmdc.201900623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 11/05/2022]
Abstract
AFMC-AIMECS meetings are internationally organized biannually by the Asian Federation for Medicinal Chemistry (AFMC) and are focused on recent studies in drug discovery and development both in academia and industry. Member organizations of the AFMC are the Pharmaceutical Society of Japan, the Chinese Pharmaceutical Association, the Royal Australian Chemical Institute, the Pharmaceutical Society of Korea, the Korean Chemical Society, the Chemical Society Located in Taipei, the Indonesian Society of Medicinal Chemistry, the Medicinal Chemistry Section of the Israel Chemical Society, and the Computer-Aided Drug Design & Development Society in Turkey. Each time, the symposium is organized within these member countries. The AIMECS 2019 symposium was held in Turkey this year, as Prof. Dr. Esin Aki-Yalcin is the current president of the AFMC (2018-2020); the next AIMECS meeting will be organized in 2021 in Tokyo, Japan. In this report, we discuss key topics at the 12th AFMC International Medicinal Chemistry Symposium - New Avenues for Design and Development of Translational Medicine (AIMECS 2019) held in Istanbul, September 8-11, 2019.
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Affiliation(s)
- Abdurrahman Olgac
- Department of Pharmaceutical Chemistry, Gazi University Faculty of Pharmacy, Emniyet Mah. Tac Sk. No.3, 06330, Yenimahalle, Ankara, Turkey.,Laboratory of Molecular Modeling, Evias Pharmaceutical R&D Ltd., Gazi Teknopark G1-101, 06830, Golbasi, Ankara, Turkey
| | - Ismail Yalcin
- Department of Pharmaceutical Chemistry, Ankara University Faculty of Pharmacy, Emniyet Mah. Degol Cd. No.4, 06560, Yenimahalle, Ankara, Turkey
| | - Esin Aki-Yalcin
- Department of Pharmaceutical Chemistry, Ankara University Faculty of Pharmacy, Emniyet Mah. Degol Cd. No.4, 06560, Yenimahalle, Ankara, Turkey
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18
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Cavasotto CN. Binding Free Energy Calculation Using Quantum Mechanics Aimed for Drug Lead Optimization. Methods Mol Biol 2020; 2114:257-268. [PMID: 32016898 DOI: 10.1007/978-1-0716-0282-9_16] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The routine use of in silico tools is already established in drug lead design. Besides the use of molecular docking methods to screen large chemical libraries and thus prioritize compounds for purchase or synthesis, more accurate calculations of protein-ligand binding free energy has shown the potential to guide lead optimization, thus saving time and resources. Theoretical developments and advances in computing power have allowed quantum mechanical-based methods applied to calculations on biomacromolecules to be increasingly explored and used, with the purpose of providing a more accurate description of protein-ligand interactions and an enhanced level of accuracy in the calculation of binding affinities. It should be noted that the quantum mechanical formulation includes, in principle, all contributions to the energy, considering terms usually neglected in molecular mechanics force fields, such as electronic polarization, metal coordination, and covalent binding; moreover, quantum mechanical approaches are systematically improvable. By treating all elements and interactions on equal footing, and avoiding the need of system-dependent parameterizations, they provide a greater degree of transferability. In this review, we illustrate the increasing relevance of quantum mechanical methods for binding free energy calculation in the context of structure-based drug lead optimization, showing representative applications of the different approaches available.
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Affiliation(s)
- Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Facultad de Ciencias Biomédicas, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina. .,Facultad de Ingeniería, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
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19
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Abstract
Computational methods are a powerful and consolidated tool in the early stage of the drug lead discovery process. Among these techniques, high-throughput molecular docking has proved to be extremely useful in identifying novel bioactive compounds within large chemical libraries. In the docking procedure, the predominant binding mode of each small molecule within a target binding site is assessed, and a docking score reflective of the likelihood of binding is assigned to them. These methods also shed light on how a given hit could be modified in order to improve protein-ligand interactions and are thus able to guide lead optimization. The possibility of reducing time and cost compared to experimental approaches made this technology highly appealing. Due to methodological developments and the increase of computational power, the application of quantum mechanical methods to study macromolecular systems has gained substantial attention in the last decade. A quantum mechanical description of the interactions involved in molecular association of biomolecules may lead to better accuracy compared to molecular mechanics, since there are many physical phenomena that cannot be correctly described within a classical framework, such as covalent bond formation, polarization effects, charge transfer, bond rearrangements, halogen bonding, and others, that require electrons to be explicitly accounted for. Considering the fact that quantum mechanics-based approaches in biomolecular simulation constitute an active and important field of research, we highlight in this work the recent developments of quantum mechanical-based molecular docking and high-throughput docking.
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Affiliation(s)
- M Gabriela Aucar
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina
| | - Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Austral Institute for Applied Artificial Intelligence, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Facultad de Ciencias Biomédicas, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
- Facultad de Ingeniería, Universidad Austral, Derqui-Pilar, Buenos Aires, Argentina.
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20
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Eyrilmez SM, Köprülüoğlu C, Řezáč J, Hobza P. Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys. Chemphyschem 2019; 20:2759-2766. [PMID: 31460692 DOI: 10.1002/cphc.201900628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Indexed: 12/11/2022]
Abstract
This paper describes the excellent performance of a newly developed scoring function (SF), based on the semiempirical QM (SQM) PM6-D3H4X method combined with the conductor-like screening implicit solvent model (COSMO). The SQM/COSMO, Amber/GB and nine widely used SFs have been evaluated in terms of ranking power on the HSP90 protein with 72 biologically active compounds and 4469 structurally similar decoys. Among conventional SFs, the highest early and overall enrichment measured by EF1 and AUC% obtained using single-scoring-function ranking has been found for Glide SP and Gold-ASP SFs, respectively (7, 75 % and 3, 76 %). The performance of other standard SFs has not been satisfactory, mostly even decreasing below random values. The SQM/COSMO SF, where P-L structures were optimised at the advanced Amber level, has resulted in a dramatic enrichment increase (47, 98 %), almost reaching the best possible receiver operator characteristic (ROC) curve. The best SQM frame thus inserts about seven times more active compounds into the selected dataset than the best standard SF.
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Affiliation(s)
- Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, CzechRepublic
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21
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Řezáč J. Description of halogen bonding in semiempirical quantum-mechanical and self-consistent charge density-functional tight-binding methods. J Comput Chem 2019; 40:1633-1642. [PMID: 30941801 DOI: 10.1002/jcc.25816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 12/20/2022]
Abstract
This article analyzes the ability of semiempirical quantum-mechanical methods (PM6 and PM7) and self-consistent charge density-functional tight-binding (SCC-DFTB) method DFTB3 to describe halogen bonds. Calculations of the electrostatic potential on the surface of molecules containing halogens show that the σ-hole could be described well in modified neglect of diatomic overlap-based methods. The situation is more complex in the case of DFTB3 where a simpler model is used for the electrostatics, but short-ranged effects are covered in the Hamiltonian. All these methods can thus capture the effects that, for example, define the geometry of halogen bonds. The interaction energies are, however, affected by generally underestimated repulsion, which has been addressed earlier by standalone empirical corrections. Another approach to correcting this issue in DFTB3 is presented here-a modification of the energies of d-orbitals on halogens yields better results than the empirical correction in DFTB3-D3X, although it remains difficult to describe halogen and hydrogen bonds simultaneously. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague, Czech Republic
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22
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Kříž K, Řezáč J. Reparametrization of the COSMO Solvent Model for Semiempirical Methods PM6 and PM7. J Chem Inf Model 2019; 59:229-235. [DOI: 10.1021/acs.jcim.8b00681] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague 2, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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23
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Guedes IA, Pereira FSS, Dardenne LE. Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges. Front Pharmacol 2018; 9:1089. [PMID: 30319422 PMCID: PMC6165880 DOI: 10.3389/fphar.2018.01089] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/07/2018] [Indexed: 12/19/2022] Open
Abstract
Structure-based virtual screening (VS) is a widely used approach that employs the knowledge of the three-dimensional structure of the target of interest in the design of new lead compounds from large-scale molecular docking experiments. Through the prediction of the binding mode and affinity of a small molecule within the binding site of the target of interest, it is possible to understand important properties related to the binding process. Empirical scoring functions are widely used for pose and affinity prediction. Although pose prediction is performed with satisfactory accuracy, the correct prediction of binding affinity is still a challenging task and crucial for the success of structure-based VS experiments. There are several efforts in distinct fronts to develop even more sophisticated and accurate models for filtering and ranking large libraries of compounds. This paper will cover some recent successful applications and methodological advances, including strategies to explore the ligand entropy and solvent effects, training with sophisticated machine-learning techniques, and the use of quantum mechanics. Particular emphasis will be given to the discussion of critical aspects and further directions for the development of more accurate empirical scoring functions.
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Affiliation(s)
- Isabella A Guedes
- Grupo de Modelagem Molecular em Sistemas Biológicos, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Felipe S S Pereira
- Grupo de Modelagem Molecular em Sistemas Biológicos, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Laurent E Dardenne
- Grupo de Modelagem Molecular em Sistemas Biológicos, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
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24
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Interface Interactions of the Bowman-Birk Inhibitor BTCI in a Ternary Complex with Trypsin and Chymotrypsin Evaluated by Semiempirical Quantum Mechanical Calculations. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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De Simone G, Angeli A, Bozdag M, Supuran CT, Winum JY, Monti SM, Alterio V. Inhibition of carbonic anhydrases by a substrate analog: benzyl carbamate directly coordinates the catalytic zinc ion mimicking bicarbonate binding. Chem Commun (Camb) 2018; 54:10312-10315. [DOI: 10.1039/c8cc05755a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
N-Unsubstituted carbamates can be used as lead compounds for the development of carbonic anhydrase inhibitors possessing a binding mode similar to bicarbonate.
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Affiliation(s)
| | - Andrea Angeli
- Neurofarba Department
- Section of Pharmaceutical and Nutriceutical Sciences
- Università degli Studi di Firenze
- Sesto Fiorentino
- Florence
| | - Murat Bozdag
- Neurofarba Department
- Section of Pharmaceutical and Nutriceutical Sciences
- Università degli Studi di Firenze
- Sesto Fiorentino
- Florence
| | - Claudiu T. Supuran
- Neurofarba Department
- Section of Pharmaceutical and Nutriceutical Sciences
- Università degli Studi di Firenze
- Sesto Fiorentino
- Florence
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- ENSCM
- Université de Montpellier
- 240 avenue du professeur Emile Jeanbrau
- 34296 Montpellier Cedex
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