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Yu S, McWilliams JC, Dirat O, Dobo KL, Kalgutkar AS, Kenyon MO, Martin MT, Watt ED, Schuler M. A Kinetic Model for Assessing Potential Nitrosamine Carcinogenicity. Chem Res Toxicol 2024. [PMID: 39075630 DOI: 10.1021/acs.chemrestox.4c00133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Understanding the potential carcinogenic potency of nitrosamines is necessary to setting acceptable intake limits. Nitrosamines and the components that can form them are commonly present in food, water, cosmetics, and tobacco. The recent observation of nitrosamines in pharmaceuticals highlighted the need for effective methods to determine acceptable intake limits. Herein, we describe two computational models that utilize properties based upon quantum mechanical calculations in conjunction with mechanistic insights and established data to determine the carcinogenic potency of a variety of common nitrosamines. These models can be applied to experimentally untested nitrosamines to aid in the establishment of acceptable intake limits.
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Affiliation(s)
- Shu Yu
- Chemical Research and Development, Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - J Christopher McWilliams
- Chemical Research and Development, Pfizer Research & Development, Groton, Connecticut 06340, United States
| | - Olivier Dirat
- CMC Advisory Office, Pfizer Global Regulatory Sciences, Sandwich CT13 9NJ, U.K
| | - Krista L Dobo
- Drug Safety Research and Development, Pfizer Research & Development-Groton Laboratories, Groton, Connecticut 06340, United States
| | - Amit S Kalgutkar
- Pharmacokinetics Dynamics and Metabolism, Pfizer Research & Development, Cambridge, Massachusetts 02139, United States
| | - Michelle O Kenyon
- Drug Safety Research and Development, Pfizer Research & Development-Groton Laboratories, Groton, Connecticut 06340, United States
| | - Matthew T Martin
- Drug Safety Research and Development, Pfizer Research & Development-Groton Laboratories, Groton, Connecticut 06340, United States
| | - Eric D Watt
- Drug Safety Research and Development, Pfizer Research & Development-Groton Laboratories, Groton, Connecticut 06340, United States
| | - Maik Schuler
- Drug Safety Research and Development, Pfizer Research & Development-Groton Laboratories, Groton, Connecticut 06340, United States
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2
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Yang W, He Y, Tian Y, Xiong H, Zhang C, Sun Y. Characterization and Mechanism of a Novel Rice Protein Peptide (AHVGMSGEEPE) Calcium Chelate in Enhancing Calcium Absorption in Caco-2 Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8569-8580. [PMID: 38563891 DOI: 10.1021/acs.jafc.3c09916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Rice protein peptides (RPP) are a potentially valuable source of high-quality calcium chelating properties. However, there is a lack of information regarding the calcium-absorption-promoting effect of RPP and its underlying mechanism. The present study adopted molecular docking methodologies to analyze the 10 most potent peptide segments from RPP. Results revealed that the peptide AHVGMSGEEPE (AHV) displayed optimal calcium binding properties (calcium-chelating capacity 55.69 ± 0.66 mg/g). Quantum chemistry analysis revealed that the AHV peptide effectively binds and forms stable complexes with calcium via the carbonyl oxygen atoms in valine at position 3 and the carbonyl of the C-terminal carboxyl group of glutamate at position 11. The spectral analysis results indicated that AHV may bind to calcium through carboxyl oxygen atoms, resulting in a transition from a smooth surface block-like structure to a dense granular structure. Furthermore, this study demonstrated that the 4 mmol/L AHV-Ca chelate (61.75 ± 13.23 μg/well) significantly increases calcium absorption compared to 1 mM CaCl2 (28.57 ± 8.59 μg/well) in the Caco-2 cell monolayer. In terms of mechanisms, the novel peptide-calcium chelate AHV-Ca derived from RPP exerts a cell-level effect by upregulating the expression of TRPV6 calcium-ion-channel-related genes and proteins (TRPV6 and Calbindin-D9k). This study provides a theoretical basis for developing functional foods with the AHV peptide as ingredients to improve calcium absorption.
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Affiliation(s)
- Wenting Yang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Yangzheng He
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Yue Tian
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Hua Xiong
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Chunbo Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
| | - Yong Sun
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, Jiangxi, China
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3
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Davis MP, Korter TM. Low-Frequency Vibrational Spectroscopy and Quantum Mechanical Simulations of the Crystalline Polymorphs of the Antiviral Drug Ribavirin. Mol Pharm 2022; 19:3385-3393. [PMID: 35950677 PMCID: PMC9449968 DOI: 10.1021/acs.molpharmaceut.2c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Crystal polymorphism is a common phenomenon in pharmaceutical
solids
and a critical issue when considering the formulation of therapeutics
since multiple polymorphs may form during drug manufacturing. Low-frequency
vibrational spectroscopy is sensitive to polymorphic content, and
in this work, terahertz time-domain spectroscopy and low-frequency
Raman spectroscopy were utilized in the study of crystalline ribavirin,
a widely applicable antiviral. Characteristic spectra with numerous
peaks in the sub-200 cm–1 region were obtained of
the more common polymorph of ribavirin (Form II). Solid-state density
functional theory (ss-DFT) simulations were then used to optimize
the crystal structure of this polymorph and calculate the frequencies
and spectral intensities of the lattice vibrations in the low-frequency
region. The near-harmonic thermal behavior of the sample with cooling
enabled excellent agreement between experiment and theory to be achieved,
emphasizing the quality of the applied model, and the observed spectral
peaks could be assigned to specific atomic motions in the solid. Form
I and Form II polymorphs of ribavirin were both investigated with
ss-DFT to understand the different aspects governing the relative
stabilities of these solids. The ss-DFT simulations of the polymorph
energies revealed that Form II is more stable at all temperatures
due to a stronger cohesive energy than Form I; however, ribavirin
in Form I has a significantly lower conformational energy. The finding
of monotropism appears to conflict with the reported enantiotropism
of the ribavirin polymorphs but ultimately confirms that crystal defects
in the real samples greatly affect the thermodynamic relationship
of the crystals.
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Affiliation(s)
- Margaret P Davis
- Department of Chemistry, Syracuse University, 1-133 Center for Science and Technology, Syracuse, New York 13244-4100, United States
| | - Timothy M Korter
- Department of Chemistry, Syracuse University, 1-133 Center for Science and Technology, Syracuse, New York 13244-4100, United States
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4
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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5
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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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6
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Wang Z, Cherukupalli S, Xie M, Wang W, Jiang X, Jia R, Pannecouque C, De Clercq E, Kang D, Zhan P, Liu X. Contemporary Medicinal Chemistry Strategies for the Discovery and Development of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2022; 65:3729-3757. [PMID: 35175760 DOI: 10.1021/acs.jmedchem.1c01758] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a major component of the highly active anti-retroviral therapy (HAART) regimen. However, the occurrence of drug-resistant strains and adverse reactions after long-term usage have inevitably compromised the clinical application of NNRTIs. Therefore, the development of novel inhibitors with distinct anti-resistance profiles and better pharmacological properties is still an enormous challenge. Herein, we summarize state-of-the-art medicinal chemistry strategies for the discovery of potent NNRTIs, such as structure-based design strategies, contemporary computer-aided drug design, covalent-binding strategies, and the application of multi-target-directed ligands. The strategies described here will facilitate the identification of promising HIV-1 NNRTIs.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Wenbo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
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7
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Calculation of Crystal-Solution Dissociation Constants. Biomolecules 2022; 12:biom12020147. [PMID: 35204648 PMCID: PMC8961641 DOI: 10.3390/biom12020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Abstract
The calculation of dissociation constants is an important problem in molecular biophysics. For such a calculation, it is important to correctly calculate both terms of the binding free energy; that is, the enthalpy and entropy of binding. Both these terms can be computed using molecular dynamics simulations, but this approach is very computationally expensive, and entropy calculations are especially slow. We develop an alternative very fast method of calculating the binding entropy and dissociation constants. The main part of our approach is based on the evaluation of movement ranges of molecules in the bound state. Then, the range of molecular movements in the bound state (here, in molecular crystals) is used for the calculation of the binding entropies and, then (using, in addition, the experimentally measured sublimation enthalpies), the crystal-to-vapor dissociation constants. Previously, we considered the process of the reversible sublimation of small organic molecules from crystals to vapor. In this work, we extend our approach by considering the dissolution of molecules, in addition to their sublimation. Similar to the sublimation case, our method shows a good correlation with experimentally measured dissociation constants at the dissolution of crystals.
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8
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Papaj K, Spychalska P, Hopko K, Kapica P, Fisher A, Lill MA, Bagrowska W, Nowak J, Szleper K, Smieško M, Kasprzycka A, Góra A. Investigation of Thiocarbamates as Potential Inhibitors of the SARS-CoV-2 Mpro. Pharmaceuticals (Basel) 2021; 14:1153. [PMID: 34832935 PMCID: PMC8621115 DOI: 10.3390/ph14111153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022] Open
Abstract
In the present study we tested, using the microscale thermophoresis technique, a small library of thionocarbamates, thiolocarbamates, sulfide and disulfide as potential lead compounds for SARS-CoV-2 Mpro drug design. The successfully identified binder is a representative of the thionocarbamates group with a high potential for future modifications aiming for higher affinity and solubility. The experimental analysis was extended by computational studies that show insufficient accuracy of the simplest and widely applied approaches and underline the necessity of applying more advanced methods to properly evaluate the affinity of potential SARS-CoV-2 Mpro binders.
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Affiliation(s)
- Katarzyna Papaj
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Patrycja Spychalska
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (P.S.); (K.H.); (A.K.)
| | - Katarzyna Hopko
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (P.S.); (K.H.); (A.K.)
| | - Patryk Kapica
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Andre Fisher
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland; (A.F.); (M.A.L.); (M.S.)
| | - Markus A. Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland; (A.F.); (M.A.L.); (M.S.)
| | - Weronika Bagrowska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Jakub Nowak
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Katarzyna Szleper
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
| | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland; (A.F.); (M.A.L.); (M.S.)
| | - Anna Kasprzycka
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (P.S.); (K.H.); (A.K.)
- Department of Chemistry, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, 44-100 Gliwice, Poland; (K.P.); (P.K.); (W.B.); (K.S.)
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9
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Bidula S, Bin Nadzirin I, Cominetti MM, Hickey H, Cullum SA, Searcey M, Schmid R, Fountain SJ. Structural basis of the negative allosteric modulation of 5-BDBD at human P2X4 receptors. Mol Pharmacol 2021; 101:33-44. [PMID: 34718224 DOI: 10.1124/molpharm.121.000402] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/17/2021] [Indexed: 11/22/2022] Open
Abstract
The P2X4 receptor is a ligand-gated ion channel activated by extracellular ATP. P2X4 activity is associated with neuropathic pain, vasodilation and pulmonary secretion and therefore of therapeutic interest. The structure-activity relationship of P2X4 antagonists is poorly understood. Here we elucidate the structure-activity of 5-BDBD at human P2X4 by combining pharmacology, electrophysiology, molecular modelling and medicinal chemistry. 5-BDBD antagonised P2X4 in a non-competitive manner but lacked effect at human P2X2. Molecular modelling and site-directed mutagenesis suggested an allosteric binding site for 5-BDBD located between two subunits in the body region of P2X4, with M109, F178, Y300 and I312 on one subunit, and R301 on the neighbouring subunit as key residues involved in antagonist binding. The bromine group of 5-BDBD was redundant for the antagonist activity of 5-BDBD, though an interaction between the carbonyl group of 5-BDBD and R301 in P2X4 was significantly associated with 5-BDBD activity. 5-BDBD could inhibit the closed channel but poorly inhibited the channel in the open/desensitising state. We hypothesize that this is due to constriction of the allosteric site following transition from closed to open channel state. We propose that M109, F178, Y300, R301 and I312 are key residues for 5-BDBD binding, provide a structural explanation of how they contribute to 5-BDBD antagonism, and highlight that the limited action of 5-BDBD on open versus closed channels is due to a conformational change in the allosteric site. Significance Statement Activity of P2X4 receptor is associated with neuropathic pain, inflammation and vasodilatation. Molecular information regarding small molecule interaction with P2X4 is very limited. Here we provide a structural explanation for the action of the small molecule antagonist 5-BDBD at the human P2X4 receptor.
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Affiliation(s)
| | | | | | - Harry Hickey
- School of Biological Sciences, University of East Anglia, United Kingdom
| | - Sean A Cullum
- School of Biological Sciences, University of East Anglia, United Kingdom
| | - Mark Searcey
- School of Pharmacy, University of East Anglia, United Kingdom
| | - Ralf Schmid
- Molecular and Cell Biology, University of Leicester, United Kingdom
| | - Samuel J Fountain
- School of Biological Sciences, University of East Anglia, United Kingdom
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10
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Wang E, Fu W, Jiang D, Sun H, Wang J, Zhang X, Weng G, Liu H, Tao P, Hou T. VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. J Chem Inf Model 2021; 61:2844-2856. [PMID: 34014672 DOI: 10.1021/acs.jcim.1c00091] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The molecular mechanics/generalized Born surface area (MM/GBSA) has been widely used in end-point binding free energy prediction in structure-based drug design (SBDD). However, in practice, it is usually being treated as a disputed method mostly because of its system dependence. Here, combining with machine-learning optimization, we developed a novel version of MM/GBSA, named variable atomic dielectric MM/GBSA (VAD-MM/GBSA), by assigning variable dielectric constants directly to the protein/ligand atoms. The new strategy exhibits markedly improved accuracy in binding affinity calculations for various protein-ligand systems and is promising to be used in the postprocessing of structure-based virtual screening. Moreover, VAD-MM/GBSA outperformed prime MM/GBSA in Schrödinger software and showed remarkable predictive performance for specific protein targets, such as POL polyprotein, human immunodeficiency virus type 1 (HIV-1) protease, etc. Our study showed that the VAD-MM/GBSA method with little extra computational overhead provides a potential replacement of the MM/GBSA in AMBER software. An online web server of VAD-MMGBSA has been developed and is now available at http://cadd.zju.edu.cn/vdgb.
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Affiliation(s)
- Ercheng Wang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Weitao Fu
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dejun Jiang
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310058, China
| | - Huiyong Sun
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Gaoqi Weng
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Peng Tao
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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11
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Awoonor-Williams E, Abu-Saleh AAAA. Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease. Phys Chem Chem Phys 2021; 23:6746-6757. [PMID: 33711090 DOI: 10.1039/d1cp00266j] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
COVID-19, the disease caused by the newly discovered coronavirus-SARS-CoV-2, has created a global health, social, and economic crisis. As of mid-January 2021, there are over 90 million confirmed cases and more than 2 million reported deaths due to COVID-19. Currently, there are very limited therapeutics for the treatment or prevention of COVID-19. For this reason, it is important to find drug targets that will lead to the development of safe and effective therapeutics against the disease. The main protease (Mpro) of the virus is an attractive target for the development of effective antiviral therapeutics because it is required for proteolytic cleavage of viral polyproteins. Furthermore, the Mpro has no human homologues, so drugs designed to bind to this target directly have less risk for off-target effects. Recently, several high-resolution crystallographic structures of the Mpro in complex with inhibitors have been determined-to guide drug development and to spur efforts in structure-based drug design. One of the primary objectives of modern structure-based drug design is the accurate prediction of receptor-ligand binding affinities for rational drug design and discovery. Here, we perform rigorous alchemical absolute binding free energy calculations and QM/MM calculations to give insight into the total binding energy of two recently crystallized inhibitors of SARS-CoV-2 Mpro, namely, N3 and α-ketoamide 13b. The total binding energy consists of both covalent and non-covalent binding components since both compounds are covalent inhibitors of the Mpro. Our results indicate that the covalent and non-covalent binding free energy contributions of both inhibitors to the Mpro target differ significantly. The N3 inhibitor has more favourable non-covalent interactions, particularly hydrogen bonding, in the binding site of the Mpro than the α-ketoamide inhibitor. Also, the Gibbs energy of reaction for the Mpro-N3 covalent adduct is greater than the Gibbs reaction energy for the Mpro-α-ketoamide covalent adduct. These differences in the covalent and non-covalent binding free energy contributions for both inhibitors could be a plausible explanation for their in vitro differences in antiviral activity. Our findings are consistent with the reversible and irreversible character of both inhibitors as reported by experiment and highlight the importance of both covalent and non-covalent binding free energy contributions to the absolute binding affinity of a covalent inhibitor towards its target. This information could prove useful in the rational design, discovery, and evaluation of potent SARS-CoV-2 Mpro inhibitors for targeted antiviral therapy.
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Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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12
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Veale CGL. Into the Fray! A Beginner's Guide to Medicinal Chemistry. ChemMedChem 2021; 16:1199-1225. [PMID: 33591595 DOI: 10.1002/cmdc.202000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville, 3209, South Africa
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13
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Dawn A, Khatri KS, Karmakar S, Deep S. Interaction of TGFβ3 ligand with its receptors type II (TβRII) and type I (TβRI): A unique mechanism of protein-protein association. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140485. [PMID: 32652126 DOI: 10.1016/j.bbapap.2020.140485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022]
Abstract
The proper orchestration of transforming growth factor beta (TGFβ) mediated signal transduction depends upon a delicate set of interactions between specific ligands and their receptors. Here we present an in-depth profiling of the binding mechanism of TGFβ3 ligand with its type II and type I receptors (TβRII and TβRI) using isothermal titration calorimetry (ITC). Studies were carried out in acidic pH as it has great physiological relevance for TGFβ3 activity. Our findings reveal an unusual positive enthalpy (∆H) compensated by a large favourable entropy (∆S) during TGFβ3-TβRII interaction. In addition to the hydrophobic effect, we propose that a distinct conformational switch from "closed" to "open" form as experienced by TGFβ3 on binding to TβRII is contributing significantly to the increase in overall entropy of the system. Binding studies of TGFβ3 and TβRII were carried out at different pH values and salt concentrations to gain further insight into the thermodynamics of the interaction. Furthermore, the importance of hydrophobic interactions on the binding affinity of TβRII with TGFβ3 was confirmed by two TβRII variants (interfacial). Finally, a distinct shift from entropy to enthalpy dominated interaction was observed upon recruitment of TβRI to the binary complex forming the ternary complex.
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Affiliation(s)
- Amrita Dawn
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Komal S Khatri
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Sandip Karmakar
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India.
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14
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Rifai EA, Ferrario V, Pleiss J, Geerke DP. Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation. J Chem Theory Comput 2020; 16:1300-1310. [PMID: 31894691 PMCID: PMC7017367 DOI: 10.1021/acs.jctc.9b00890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Calculating free energies of binding (ΔGbind) between ligands and their target protein is of major interest to drug discovery and safety, yet it is still associated with several challenges and difficulties. Linear interaction energy (LIE) is an efficient in silico method for ΔGbind computation. LIE models can be trained and used to directly calculate binding affinities from interaction energies involving ligands in the bound and unbound states only, and LIE can be combined with statistical weighting to calculate ΔGbind for flexible proteins that may bind their ligands in multiple orientations. Here, we investigate if LIE predictions can be effectively improved by explicitly including the entropy of (de)solvation into our free-energy calculations. For that purpose, we combine LIE calculations for the protein-ligand-bound state with explicit free-energy perturbation to rigorously compute the unbound ligand's solvation free energy. We show that for 28 Cytochrome P450 2A6 (CYP2A6) ligands, coupling LIE with alchemical solvation free-energy calculation helps to improve obtained correlation between computed and reference (experimental) binding data.
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Affiliation(s)
- Eko Aditya Rifai
- AIMMS Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry , Universität Stuttgart , Allmandring 31 , 70569 Stuttgart , Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry , Universität Stuttgart , Allmandring 31 , 70569 Stuttgart , Germany
| | - Daan P Geerke
- AIMMS Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
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15
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16
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Santarsia S, Grosso AS, Trovão F, Jiménez-Barbero J, Carvalho AL, Nativi C, Marcelo F. Molecular Recognition of a Thomsen-Friedenreich Antigen Mimetic Targeting Human Galectin-3. ChemMedChem 2018; 13:2030-2036. [PMID: 30094951 DOI: 10.1002/cmdc.201800525] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Indexed: 11/11/2022]
Abstract
Overexpression of the Thomsen-Friedenreich (TF) antigen in cell membrane proteins occurs in 90 % of adenocarcinomas. Additionally, the binding of the TF antigen to human galectin-3 (Gal-3), also frequently overexpressed in malignancy, promotes cancer progression and metastasis. In this context, structures that interfere with this specific interaction have the potential to prevent cancer metastasis. A multidisciplinary approach combining the optimized synthesis of a TF antigen mimetic with NMR, X-ray crystallography methods, and isothermal titration calorimetry assays was used to unravel the molecular structural details that govern the Gal-3/TF mimetic interaction. The TF mimetic has a binding affinity for Gal-3 similar to that of the TF natural antigen and retains the binding epitope and bioactive conformation observed for the native antigen. Furthermore, from a thermodynamic perspective, a decrease in the enthalpic contribution was observed for the Gal-3/TF mimetic complex; however, this behavior is compensated by a favorable gain in entropy. From a structural perspective, these results establish our TF mimetic as a scaffold to design multivalent solutions to potentially interfere with Gal-3 aberrant interactions and for likely use in hampering Gal-3-mediated cancer cell adhesion and metastasis.
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Affiliation(s)
- Sabrina Santarsia
- Department of Chemistry Ugo Schiff, University of Florence, Via della Lastruccia, 13-50019, Sesto Fiorentino, Italy
| | - Ana Sofia Grosso
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Filipa Trovão
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC-bioGUNE Bizkaia, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48005, Bilbao, Spain.,Department of Organic Chemistry II, EHU-UPV, 48040, Leioa, Spain
| | - Ana Luísa Carvalho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Cristina Nativi
- Department of Chemistry Ugo Schiff, University of Florence, Via della Lastruccia, 13-50019, Sesto Fiorentino, Italy
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade De Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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17
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Ravindra M, Wilson MR, Tong N, O'Connor C, Karim M, Polin L, Wallace-Povirk A, White K, Kushner J, Hou Z, Matherly LH, Gangjee A. Fluorine-Substituted Pyrrolo[2,3- d]Pyrimidine Analogues with Tumor Targeting via Cellular Uptake by Folate Receptor α and the Proton-Coupled Folate Transporter and Inhibition of de Novo Purine Nucleotide Biosynthesis. J Med Chem 2018; 61:4228-4248. [PMID: 29701475 DOI: 10.1021/acs.jmedchem.8b00408] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Novel fluorinated 2-amino-4-oxo-6-substituted pyrrolo[2,3- d]pyrimidine analogues 7-12 were synthesized and tested for selective cellular uptake by folate receptors (FRs) α and β or the proton-coupled folate transporter (PCFT) and for antitumor efficacy. Compounds 8, 9, 11, and 12 showed increased in vitro antiproliferative activities (∼11-fold) over the nonfluorinated analogues 2, 3, 5, and 6 toward engineered Chinese hamster ovary and HeLa cells expressing FRs or PCFT. Compounds 8, 9, 11, and 12 also inhibited proliferation of IGROV1 and A2780 epithelial ovarian cancer cells; in IGROV1 cells with knockdown of FRα, 9, 11, and 12 showed sustained inhibition associated with uptake by PCFT. All compounds inhibited glycinamide ribonucleotide formyltransferase, a key enzyme in the de novo purine biosynthesis pathway. Molecular modeling studies validated in vitro cell-based results. NMR evidence supports the presence of an intramolecular fluorine-hydrogen bond. Potent in vivo efficacy of 11 was established with IGROV1 xenografts in severe compromised immunodeficient mice.
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Affiliation(s)
- Manasa Ravindra
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences , Duquesne University , 600 Forbes Avenue , Pittsburgh , Pennsylvania 15282 , United States
| | - Mike R Wilson
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences , Duquesne University , 600 Forbes Avenue , Pittsburgh , Pennsylvania 15282 , United States.,Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Nian Tong
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences , Duquesne University , 600 Forbes Avenue , Pittsburgh , Pennsylvania 15282 , United States
| | - Carrie O'Connor
- Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Mohammad Karim
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences , Duquesne University , 600 Forbes Avenue , Pittsburgh , Pennsylvania 15282 , United States
| | - Lisa Polin
- Molecular Therapeutics Program , Barbara Ann Karmanos Cancer Institute , 421 East Canfield Street , Detroit , Michigan 48201 , United States.,Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Adrianne Wallace-Povirk
- Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Kathryn White
- Molecular Therapeutics Program , Barbara Ann Karmanos Cancer Institute , 421 East Canfield Street , Detroit , Michigan 48201 , United States.,Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Juiwanna Kushner
- Molecular Therapeutics Program , Barbara Ann Karmanos Cancer Institute , 421 East Canfield Street , Detroit , Michigan 48201 , United States.,Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Zhanjun Hou
- Molecular Therapeutics Program , Barbara Ann Karmanos Cancer Institute , 421 East Canfield Street , Detroit , Michigan 48201 , United States.,Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Larry H Matherly
- Molecular Therapeutics Program , Barbara Ann Karmanos Cancer Institute , 421 East Canfield Street , Detroit , Michigan 48201 , United States.,Department of Oncology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States.,Department of Pharmacology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences , Duquesne University , 600 Forbes Avenue , Pittsburgh , Pennsylvania 15282 , United States
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18
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Garbuzynskiy SO, Finkelstein AV. Evaluation of the Accuracy of Calculation of the Standard Binding Entropy of Molecules from their Average Mobility in Molecular Crystals. Mol Biol 2018. [DOI: 10.1134/s0026893318010053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Garbuzynskiy SO, Finkelstein AV. Sublimation Entropy and Dissociation Constants Prediction by Quantitative Evaluation of Molecular Mobility in Crystals. J Phys Chem Lett 2017; 8:2758-2763. [PMID: 28558247 DOI: 10.1021/acs.jpclett.7b00915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Prediction of binding free energies (or dissociation constants) is a crucial challenge for computational biochemistry. One of the main problems here consists in fast and accurate evaluation of binding entropy, which is far more time-consuming than evaluation of binding enthalpy. Here, we offer a fast and rather accurate approach to evaluate the sublimation entropy (i.e., entropy of binding of a vapor molecule to a crystal, taken with the opposite sign) from the average range of molecular movements in the solid state. To estimate this range (and the corresponding amplitude), we considered equilibrium sublimation of small organic molecules from molecular crystals. The calculations were based on experimental data on the sublimation enthalpy, pressure of saturated vapor, and structural characteristics of the molecule in question. The resulting average amplitude (0.17 ± 0.01 Å) of molecular movements in crystals was used to predict sublimation entropies and dissociation constants for sublimation of 28 molecular crystals. The results of these predictions are in close agreement with experimental values.
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Affiliation(s)
- Sergiy O Garbuzynskiy
- Laboratory of Protein Physics, Institute of Protein Research, Russian Academy of Sciences , 4 Institutskaya Street, 142290 Pushchino, Moscow Region, Russia
| | - Alexei V Finkelstein
- Laboratory of Protein Physics, Institute of Protein Research, Russian Academy of Sciences , 4 Institutskaya Street, 142290 Pushchino, Moscow Region, Russia
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20
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Procacci P, Chelli R. Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories. J Chem Theory Comput 2017; 13:1924-1933. [DOI: 10.1021/acs.jctc.6b01192] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Via Lastruccia
n. 3, Sesto
Fiorentino I-50019, Italy
| | - Riccardo Chelli
- Department of Chemistry, University of Florence, Via Lastruccia
n. 3, Sesto
Fiorentino I-50019, Italy
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21
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Ben-Shalom IY, Pfeiffer-Marek S, Baringhaus KH, Gohlke H. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations. J Chem Inf Model 2017; 57:170-189. [DOI: 10.1021/acs.jcim.6b00373] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ido Y. Ben-Shalom
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Stefania Pfeiffer-Marek
- LGCR/Pharmaceutical
Sciences Operations, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Karl-Heinz Baringhaus
- R&D Resources/Site Direction, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Department of Mathematics
and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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22
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Wang C, Nguyen PH, Pham K, Huynh D, Le TBN, Wang H, Ren P, Luo R. Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. J Comput Chem 2016; 37:2436-46. [PMID: 27510546 PMCID: PMC5018451 DOI: 10.1002/jcc.24467] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/13/2016] [Indexed: 11/07/2022]
Abstract
Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) methods have become widely adopted in estimating protein-ligand binding affinities due to their efficiency and high correlation with experiment. Here different computational alternatives were investigated to assess their impact to the agreement of MMPBSA calculations with experiment. Seven receptor families with both high-quality crystal structures and binding affinities were selected. First the performance of nonpolar solvation models was studied and it was found that the modern approach that separately models hydrophobic and dispersion interactions dramatically reduces RMSD's of computed relative binding affinities. The numerical setup of the Poisson-Boltzmann methods was analyzed next. The data shows that the impact of grid spacing to the quality of MMPBSA calculations is small: the numerical error at the grid spacing of 0.5 Å is already small enough to be negligible. The impact of different atomic radius sets and different molecular surface definitions was further analyzed and weak influences were found on the agreement with experiment. The influence of solute dielectric constant was also analyzed: a higher dielectric constant generally improves the overall agreement with experiment, especially for highly charged binding pockets. The data also showed that the converged simulations caused slight reduction in the agreement with experiment. Finally the direction of estimating absolute binding free energies was briefly explored. Upon correction of the binding-induced rearrangement free energy and the binding entropy lost, the errors in absolute binding affinities were also reduced dramatically when the modern nonpolar solvent model was used, although further developments were apparently necessary to further improve the MMPBSA methods. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, Irvine, California, 92697
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
- Department of Physics and Astronomy, University of California, Irvine, California, 92697
| | - Peter H Nguyen
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | - Kevin Pham
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | - Danielle Huynh
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | | | - Hongli Wang
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas, Austin, Texas, 78712
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, Irvine, California, 92697.
- Department of Molecular Biology and Biochemistry, Irvine, California, 92697.
- Department of Chemical Engineering and Materials Science, Irvine, California, 92697.
- Department of Biomedical Engineering, University of California, Irvine, California, 92697.
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23
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Montalvo-Acosta JJ, Cecchini M. Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding. Mol Inform 2016; 35:555-567. [PMID: 27554325 DOI: 10.1002/minf.201600052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/01/2016] [Indexed: 11/08/2022]
Abstract
The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline.
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Affiliation(s)
- Joel José Montalvo-Acosta
- Laboratoire d'Ingénierie des Fonctions Moléculaires ISIS, UMR 7006 CNRS, Université de Strasbourg, F-67083, Strasbourg Cedex, France
| | - Marco Cecchini
- Laboratoire d'Ingénierie des Fonctions Moléculaires ISIS, UMR 7006 CNRS, Université de Strasbourg, F-67083, Strasbourg Cedex, France
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24
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Garbuzynskiy SO, Finkelstein AV. Calculation of mobility and entropy of the binding of molecules by crystals. Mol Biol 2016. [DOI: 10.1134/s0026893316020060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Procacci P. Reformulating the entropic contribution in molecular docking scoring functions. J Comput Chem 2016; 37:1819-27. [DOI: 10.1002/jcc.24397] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/30/2016] [Accepted: 04/10/2016] [Indexed: 11/08/2022]
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26
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Sun H, Li Y, Tian S, Xu L, Hou T. Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. Phys Chem Chem Phys 2015; 16:16719-29. [PMID: 24999761 DOI: 10.1039/c4cp01388c] [Citation(s) in RCA: 549] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
By using different evaluation strategies, we systemically evaluated the performance of Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodologies based on more than 1800 protein-ligand crystal structures in the PDBbind database. The results can be summarized as follows: (1) for the one-protein-family/one-binding-ligand case which represents the unbiased protein-ligand complex sampling, both MM/GBSA and MM/PBSA methodologies achieve approximately equal accuracies at the interior dielectric constant of 4 (with rp = 0.408 ± 0.006 of MM/GBSA and rp = 0.388 ± 0.006 of MM/PBSA based on the minimized structures); while for the total dataset (1864 crystal structures), the overall best Pearson correlation coefficient (rp = 0.579 ± 0.002) based on MM/GBSA is better than that of MM/PBSA (rp = 0.491 ± 0.003), indicating that biased sampling may significantly affect the accuracy of the predicted result (some protein families contain too many instances and can bias the overall predicted accuracy). Therefore, family based classification is needed to evaluate the two methodologies; (2) the prediction accuracies of MM/GBSA and MM/PBSA for different protein families are quite different with rp ranging from 0 to 0.9, whereas the correlation and ranking scores (an averaged rp/rs over a list of protein folds and also representing the unbiased sampling) given by MM/PBSA (rp-score = 0.506 ± 0.050 and rs-score = 0.481 ± 0.052) are comparable to those given by MM/GBSA (rp-score = 0.516 ± 0.047 and rs-score = 0.463 ± 0.047) at the fold family level; (3) for the overall prediction accuracies, molecular dynamics (MD) simulation may not be quite necessary for MM/GBSA (rp-minimized = 0.579 ± 0.002 and rp-1ns = 0.564 ± 0.002), but is needed for MM/PBSA (rp-minimized = 0.412 ± 0.003 and rp-1ns = 0.491 ± 0.003). However, for the individual systems, whether to use MD simulation is depended. (4) both MM/GBSA and MM/PBSA may be unable to give successful predictions for the ligands with high formal charges, with the Pearson correlation coefficient ranging from 0.621 ± 0.003 (neutral ligands) to 0.125 ± 0.142 (ligands with a formal charge of 5). Therefore, it can be summarized that, although MM/GBSA and MM/PBSA perform similarly in the unbiased dataset, for the currently available crystal structures in the PDBbind database, compared with MM/GBSA, which may be used in multi-target comparisons, MM/PBSA is more sensitive to the investigated systems, and may be more suitable for individual-target-level binding free energy ranking. This study may provide useful guidance for the post-processing of docking based studies.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu 215123, China.
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27
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Fong CW. Binding energies of tyrosine kinase inhibitors: Error assessment of computational methods for imatinib and nilotinib binding. Comput Biol Chem 2015; 58:40-54. [PMID: 26025598 DOI: 10.1016/j.compbiolchem.2015.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 05/09/2015] [Accepted: 05/13/2015] [Indexed: 11/30/2022]
Abstract
The binding energies of imatinib and nilotinib to tyrosine kinase have been determined by quantum mechanical (QM) computations, and compared with literature binding energy studies using molecular mechanics (MM). The potential errors in the computational methods include these critical factors. Errors in X-ray structures such as structural distortions and steric clashes give unrealistically high van der Waals energies, and erroneous binding energies.MM optimization gives a very different configuration to the QM optimization for nilotinib, whereas the imatinib ion gives similar configurations. Solvation energies are a major component of the overall binding energy. The QM based solvent model (PCM/SMD) gives different values from those used in the implicit PBSA solvent MM models. A major error in inhibitor—kinase binding lies in the non-polar solvation terms. Solvent transfer free energies and the required empirical solvent accessible surface area factors for nilotinib and imatinib ion to give the transfer free energies have been reverse calculated. These values differ from those used in the MM PBSA studies.An intertwined desolvation—conformational binding selectivity process is a balance of thermodynamic desolvation and intramolecular conformational kinetic control.The configurational entropies (TΔS) are minor error sources.
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Abstract
INTRODUCTION The molecular mechanics energies combined with the Poisson-Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor-ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success. AREAS COVERED The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications. EXPERT OPINION MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. Moreover, there are many variants of the method and their performance varies strongly with the tested system. Likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results.
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Affiliation(s)
- Samuel Genheden
- University of Southampton, School of Chemistry, Highfield, SO17 1BJ, Southampton, UK
| | - Ulf Ryde
- Lund University, Chemical Centre, Department of Theoretical Chemistry, P. O. Box 124, SE-221 00 Lund, Sweden+46 46 2224502; +46 46 2228648;
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Mata-Munguía C, Escoto-Delgadillo M, Torres-Mendoza B, Flores-Soto M, Vázquez-Torres M, Gálvez-Gastelum F, Viniegra-Osorio A, Castillero-Manzano M, Vázquez-Valls E. Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis. BMC Bioinformatics 2014; 15:72. [PMID: 24629078 PMCID: PMC4003850 DOI: 10.1186/1471-2105-15-72] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 03/05/2014] [Indexed: 11/22/2022] Open
Abstract
Background The correlations of genotypic and phenotypic tests with treatment, clinical history and the significance of mutations in viruses of HIV-infected patients are used to establish resistance mutations to protease inhibitors (PIs). Emerging mutations in human immunodeficiency virus type 1 (HIV-1) protease confer resistance to PIs by inducing structural changes at the ligand interaction site. The aim of this study was to establish an in silico structural relationship between natural HIV-1 polymorphisms and unusual HIV-1 mutations that confer resistance to PIs. Results Protease sequences isolated from 151 Mexican HIV-1 patients that were naïve to, or subjected to antiretroviral therapy, were examined. We identified 41 unrelated resistance mutations with a prevalence greater than 1%. Among these mutations, nine exhibited positive selection, three were natural polymorphisms (L63S/V/H) in a codon associated with drug resistance, and six were unusual mutations (L5F, D29V, L63R/G, P79L and T91V). The D29V mutation, with a prevalence of 1.32% in the studied population, was only found in patients treated with antiretroviral drugs. Using in silico modelling, we observed that D29V formed unstable protease complexes when were docked with lopinavir, saquinavir, darunavir, tipranavir, indinavir and atazanavir. Conclusions The structural correlation of natural polymorphisms and unusual mutations with drug resistance is useful for the identification of HIV-1 variants with potential resistance to PIs. The D29V mutation likely confers a selection advantage in viruses; however, in silico, presence of this mutation results in unstable enzyme/PI complexes, that possibly induce resistance to PIs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Eduardo Vázquez-Valls
- Laboratorio de Inmunodeficiencias y Retrovirus Humanos, Centro de Investigación Biomédica de Occidente, CMNO, IMSS, Guadalajara 44340, México.
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30
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Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase. J Mol Graph Model 2013; 45:13-25. [DOI: 10.1016/j.jmgm.2013.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/30/2013] [Indexed: 12/28/2022]
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31
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Deeb SE, Wätzig H, El-Hady DA. Capillary electrophoresis to investigate biopharmaceuticals and pharmaceutically-relevant binding properties. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Wang L, Deng Y, Knight JL, Wu Y, Kim B, Sherman W, Shelley JC, Lin T, Abel R. Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors. J Chem Theory Comput 2013; 9:1282-93. [PMID: 26588769 DOI: 10.1021/ct300911a] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Lingle Wang
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Yuqing Deng
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Jennifer L. Knight
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Yujie Wu
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Byungchan Kim
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Woody Sherman
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - John C. Shelley
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Teng Lin
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Robert Abel
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
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33
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Greenidge PA, Kramer C, Mozziconacci JC, Wolf RM. MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement. J Chem Inf Model 2012; 53:201-9. [DOI: 10.1021/ci300425v] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Paulette A. Greenidge
- Novartis Institutes
for Biomedical Research, Novartis Pharma AG, Forum 1, Novartis Campus, CH 4056 Basel, Switzerland
| | - Christian Kramer
- Novartis Institutes
for Biomedical Research, Novartis Pharma AG, Forum 1, Novartis Campus, CH 4056 Basel, Switzerland
| | | | - Romain M. Wolf
- Novartis Institutes
for Biomedical Research, Novartis Pharma AG, Forum 1, Novartis Campus, CH 4056 Basel, Switzerland
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An efficient synthesis of 3-OBn-6β,14-epoxy-bridged opiates from naltrexone and identification of a related dual MOR inverse agonist/KOR agonist. Bioorg Med Chem Lett 2012; 22:6801-5. [DOI: 10.1016/j.bmcl.2012.06.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/08/2012] [Accepted: 06/11/2012] [Indexed: 12/14/2022]
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35
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Li X, Fu Z, Merz KM. QM/MM refinement and analysis of protein bound retinoic acid. J Comput Chem 2012; 33:301-10. [PMID: 22108894 PMCID: PMC3240731 DOI: 10.1002/jcc.21978] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/13/2011] [Accepted: 09/28/2011] [Indexed: 11/12/2022]
Abstract
Retinoic acid (RA) is a vitamin A derivative, which modifies the appearance of fine wrinkles and roughness of facial skin and treats acne and activates gene transcription by binding to heterodimers of the retinoic acid receptor (RAR) and the retinoic X receptor (RXR). There are series of protein bound RA complexes available in the protein databank (PDB), which provides a broad range of information about the different bioactive conformations of RA. To gain further insights into the observed bioactive RA conformations we applied quantum mechanic (QM)/molecular mechanic (MM) approaches to re-refine the available RA protein-ligand complexes. MP2 complete basis set (CBS) extrapolations single energy calculations are also carried out for both the experimental conformations and QM optimized geometries of RA in the gas as well as solution phase. The results demonstrate that the re-refined structures show better geometries for RA than seen in the originally deposited PDB structures through the use of QMs for the ligand in the X-ray refinement procedure. QM/MM re-refined conformations also reduced the computed strain energies found in the deposited crystal conformations for RA. Finally, the dependence of ligand strain on resolution is analyzed. It is shown that ligand strain is not converged in our calculations and is likely an artifact of the typical resolutions employed to study protein-ligand complexes.
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Affiliation(s)
- Xue Li
- Department of Chemistry, Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
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36
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Gallicchio E. Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase. ACTA ACUST UNITED AC 2012; 2:7-22. [PMID: 22708073 DOI: 10.4236/cmb.2012.21002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The results of computer simulations of the binding of etravirine (TMC125) and rilpivirine (TMC278) to HIV reverse transcriptase are reported. It is confirmed that consistent binding free energy estimates are obtained with or without the application of torsional restraints when the free energies of imposing the restraints are taken into account. The restraints have a smaller influence on the thermodynamics and apparent kinetics of binding of TMC125 compared to the more flexible TMC278 inhibitor. The concept of the reorganization free energy of binding is useful to understand and categorize these effects. Contrary to expectations, the use of conformational restraints did not consistently enhance convergence of binding free energy estimates due to suppression of binding/unbinding pathways and due to the influence of rotational degrees of freedom not directly controlled by the restraints. Physical insights concerning the thermodynamic driving forces for binding and the role of "jiggling" and "wiggling" motion of the ligands are discussed. Based on these insights we conclude that an ideal inhibitor, if chemically realizable, would possess the electrostatic charge distribution of TMC125, so as to form strong interactions with the receptor, and the larger and more flexible substituents of TMC278, so as to minimize reorganization free energy penalties and the effects of resistance mutations, suitably modified, as in TMC125, so as to disfavor the formation of non-binding competent extended conformations when free in solution.
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Affiliation(s)
- Emilio Gallicchio
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, Piseatawav, NJ 08854
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37
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Lapelosa M, Gallicchio E, Levy RM. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J Chem Theory Comput 2011; 8:47-60. [PMID: 22368530 DOI: 10.1021/ct200684b] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations.
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Affiliation(s)
- Mauro Lapelosa
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, Piscataway, NJ 08854
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38
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Park MS, Gao C, Stern HA. Estimating binding affinities by docking/scoring methods using variable protonation states. Proteins 2011; 79:304-14. [PMID: 21058298 DOI: 10.1002/prot.22883] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To investigate the effects of multiple protonation states on protein-ligand recognition, we generated alternative protonation states for selected titratable groups of ligands and receptors. The selection of states was based on the predicted pK(a) of the unbound receptor and ligand and the proximity of titratable groups of the receptor to the binding site. Various ligand tautomer states were also considered. An independent docking calculation was run for each state. Several protocols were examined: using an ensemble of all generated states of ligand and receptor, using only the most probable state of the unbound ligand/receptor, and using only the state giving the most favorable docking score. The accuracies of these approaches were compared, using a set of 176 protein-ligand complexes (15 receptors) for which crystal structures and measured binding affinities are available. The best agreement with experiment was obtained when ligand poses from experimental crystal structures were used. For 9 of 15 receptors, using an ensemble of all generated protonation states of the ligand and receptor gave the best correlation between calculated and measured affinities.
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Affiliation(s)
- Min-Sun Park
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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39
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Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P. Virtual screening using molecular simulations. Proteins 2011; 79:1940-51. [PMID: 21491494 DOI: 10.1002/prot.23018] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/24/2011] [Accepted: 02/05/2011] [Indexed: 11/05/2022]
Abstract
Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) surface area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A, and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range of 0.56-0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data whereas the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery.
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Affiliation(s)
- Tianyi Yang
- Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA
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40
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Gallicchio E, Levy RM. Advances in all atom sampling methods for modeling protein-ligand binding affinities. Curr Opin Struct Biol 2011; 21:161-6. [PMID: 21339062 DOI: 10.1016/j.sbi.2011.01.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/25/2011] [Accepted: 01/27/2011] [Indexed: 01/23/2023]
Abstract
Conformational dynamics plays a fundamental role in the regulation of molecular recognition processes. Conformational heterogeneity and entropy variations upon binding, although not always evident from the analysis of structural data, can substantially affect affinity and specificity. Computer modeling is able to provide some of the most direct insights into these aspects of molecular recognition. We review recent physics-based computational studies that employ advanced conformational sampling algorithms and effective potentials to model the three main classes of degrees of freedom relevant to the binding process: ligand positioning relative to the receptor, ligand and receptor internal reorganization, and hydration. Collectively these studies show that all of these elements are important for proper modeling of protein-ligand interactions.
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Affiliation(s)
- Emilio Gallicchio
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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41
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Gallicchio E, Levy RM. Recent theoretical and computational advances for modeling protein-ligand binding affinities. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 85:27-80. [PMID: 21920321 DOI: 10.1016/b978-0-12-386485-7.00002-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We review recent theoretical and algorithmic advances for the modeling of protein ligand binding free energies. We first describe a statistical mechanics theory of noncovalent association, with particular focus on deriving the fundamental formulas on which computational methods are based. The second part reviews the main computational models and algorithms in current use or development, pointing out the relations with each other and with the theory developed in the first part. Particular emphasis is given to the modeling of conformational reorganization and entropic effect. The methods reviewed are free energy perturbation, double decoupling, the Binding Energy Distribution Analysis Method, the potential of mean force method, mining minima and MM/PBSA. These models have different features and limitations, and their ranges of applicability vary correspondingly. Yet their origins can all be traced back to a single fundamental theory.
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Affiliation(s)
- Emilio Gallicchio
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey, USA
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