1
|
Masuda T, Suzuki M, Yamasaki M, Mikami B. Subatomic structure of orthorhombic thaumatin at 0.89 Å reveals that highly flexible conformations are crucial for thaumatin sweetness. Biochem Biophys Res Commun 2024; 703:149601. [PMID: 38364680 DOI: 10.1016/j.bbrc.2024.149601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
Thaumatin is a sweet-tasting protein that elicits a sweet taste at a threshold of approximately 50 nM. Structure-sweetness relationships in thaumatin suggest that the basicity of two amino acids residues, Arg82 and Lys67, are particularly responsible for sweetness. Using tetragonal crystals, our structural analysis suggested that flexible sidechain conformations of these two residues play an important role in sweetness. However, in tetragonal crystals, Arg82 is adjacent to symmetry-related residues, and its flexibility is relatively restrained by the crystal packing. To reduce and diminish these symmetry-related effects, orthorhombic crystals were prepared, and their structures were successfully determined at a resolution of 0.89 Å. Within the orthorhombic lattice, two alternative conformations were more clearly visible at Lys67 than in a tetragonal system. Interestingly, for the first time, three alternative conformations at Arg82 were only found in an orthorhombic system. These results suggest the importance of flexible conformations in sweetness determinants. Such subtle structural variations might serve to adjust the complementarity of the electrostatic potentials of sweet receptors, thereby eliciting the potent sweet taste of thaumatin.
Collapse
Affiliation(s)
- Tetsuya Masuda
- Department of Food Sciences and Human Nutrition, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan; Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayuki Yamasaki
- Department of Food Sciences and Human Nutrition, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan; Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| |
Collapse
|
2
|
Herrmann B, Svatunek D. Directionality of Halogen-Bonds: Insights from 2D Energy Decomposition Analysis. Chem Asian J 2024:e202301106. [PMID: 38390759 DOI: 10.1002/asia.202301106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/25/2024] [Indexed: 02/24/2024]
Abstract
Halogen bonds are typically observed to have a linear arrangement with a 180° angle between the nucleophile and the halogen bond acceptor X-R. This linearity is commonly explained using the σ-hole model, although there have been alternative explanations involving exchange repulsion forces. We employ two-dimensional Distortion/Interaction and Energy Decomposition Analysis to examine the archetypal H3 N⋯X2 halogen bond systems. Our results indicate that although halogen bonds are predominantly electrostatic, their directionality is largely due to decreased Pauli repulsion in linear configurations as opposed to angled ones in the I2 and Br2 systems. As we move to the smaller halogens, Cl2 and F2 , the influence of Pauli repulsion diminishes, and the energy surface is shaped by orbital interactions and electrostatic forces. These results support the role of exchange repulsion forces in influencing the directionality of strong halogen bonds. Additionally, we demonstrate that the 2D Energy Decomposition Analysis is a useful tool for enhancing our understanding of the nature of potential energy surfaces in noncovalent interactions.
Collapse
Affiliation(s)
- Barbara Herrmann
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Dennis Svatunek
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| |
Collapse
|
3
|
Bahl AS, Verma VK, Prajapati V, Bhatia J, Arya DS. In-silico Assessment of Polyherbal Oils as Anti-diabetic Therapeutics. Curr Comput Aided Drug Des 2024; 20:673-684. [PMID: 37873913 DOI: 10.2174/0115734099267172231012070353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Diabetes mellitus (DM) is characterized by elevated blood glucose levels either due to insufficient insulin production, defective insulin action, or both. It affects nearly 537 million individuals worldwide. Pharmacological treatment involves the use of oral antidiabetic agents as mono or combination therapy that effectively aids in controlling hyperglycemia. Despite providing therapeutic benefits, these medications limit their use owing to adverse side effects. Certain natural products, including essential oils, have promising anti-diabetic properties. OBJECTIVE The present study explores the effectiveness of two polyherbal oils and their compound towards the treatment of DM based on an In-silico approach to drug investigations Methods: Compounds present in the polyherbal oil formulation were identified using GCMS/ MS analysis. Selected compounds undergo molecular docking with the receptor, and proteins play an important role in DM. The potential compounds showing higher interactions than the known inhibitors or inducers were evaluated using molecular dynamic simulations RMSD value. RESULTS The compounds identified through GC-MS analysis possess anti-diabetic and antiinflammatory properties. With the aid of in silico prediction methods, compounds such as geraniol, cinnamaldehyde, anethole, caryophyllene, terpinyl acetate, cymene, linalool, menthol, Phenol,2-methoxy-3-(2-propenyl), and 2,6- octadienal,3,7-dimethyl were identified as strong binders of GLUT4 and insulin receptor proteins. Geraniol and Phenol,2-methoxy-3-(2-propenyl) interaction with GLUT4 were of particular importance owing to their conformational stability. CONCLUSION Our data suggest an agonistic effect of compounds on target proteins aiding in enhanced insulin activity and could serve as a potential anti-diabetic agent.
Collapse
Affiliation(s)
- Amul S Bahl
- Department of Research, Development and Innovation, God's Own Store LLP, New Delhi, 110065, India
| | - Vipin Kumar Verma
- Deptartment of Pharmacology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Vaishali Prajapati
- Deptartment of Pharmacology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Jagriti Bhatia
- Deptartment of Pharmacology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Dharamvir Singh Arya
- Deptartment of Pharmacology, All India Institute of Medical Sciences, New Delhi, 110029, India
| |
Collapse
|
4
|
Catapano L, Long F, Yamashita K, Nicholls RA, Steiner RA, Murshudov GN. Neutron crystallographic refinement with REFMAC5 from the CCP4 suite. Acta Crystallogr D Struct Biol 2023; 79:1056-1070. [PMID: 37921806 PMCID: PMC7615533 DOI: 10.1107/s2059798323008793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.
Collapse
Affiliation(s)
- Lucrezia Catapano
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Keitaro Yamashita
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
5
|
Chiba K, Matsui T, Chatake T, Ohhara T, Tanaka I, Yutani K, Niimura N. Site-specific relaxation of peptide bond planarity induced by electrically attracted proton/deuteron observed by neutron crystallography. Protein Sci 2023; 32:e4765. [PMID: 37624071 PMCID: PMC10510461 DOI: 10.1002/pro.4765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/25/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
In structural biology, peptide bonds, fundamental linkages between hundreds of amino acids, of which a protein molecule is composed, have been commonly treated as a plane structure just as Linus Pauling et al. proposed. In this paper, a site-specific peptide bond relaxation mechanism by deuterons whose localization has been suggested by neutron crystallography is proposed. Such deuteron was observed as an arm of neutron scattering length density protruding from the carbonyl oxygen atoms in the main chain in the omit map drawn by neutron crystallography of human lysozyme. Our comprehensive study using x-ray and neutron diffraction and 15 N chemical shifts of individual amide nitrogen atoms within the same peptide bond strongly suggests the relaxation of the electronic resonance structure because of site-specific modulation by protons/deuterons localized on the electron orbital of the carbonyl oxygen. All experimental data used in this examination were obtained at room temperature, which is preferable for enzymatic activity. Such a close interaction between the electron resonance structure of a peptide bond and the exchangeable protons/deuterons well agreed with that observed in an intermediate state in an amide hydrolytic reaction simulated by the ab-initio calculation including water molecules.
Collapse
Affiliation(s)
- Kaori Chiba
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Department of Industrial EngineeringNational Institute of Technology, Ibaraki CollegeHitachinakaIbarakiJapan
| | - Takuro Matsui
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
| | - Toshiyuki Chatake
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversitySennanOsakaJapan
| | - Takashi Ohhara
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Neutron Science Section, J‐PARC CenterJapan Atomic Energy AgencyTokaiIbarakiJapan
| | - Ichiro Tanaka
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Graduate School of Science and EngineeringIbaraki UniversityHitachiIbarakiJapan
- Frontier Research Center for Applied Atomic SciencesIbaraki UniversityHitachiIbarakiJapan
| | | | - Nobuo Niimura
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Frontier Research Center for Applied Atomic SciencesIbaraki UniversityHitachiIbarakiJapan
| |
Collapse
|
6
|
Ramírez-Velásquez IM, Bedoya-Calle ÁH, Vélez E, Caro-Lopera FJ. Dissociation Mode of the O-H Bond in Betanidin, pK a-Clusterization Prediction, and Molecular Interactions via Shape Theory and DFT Methods. Int J Mol Sci 2023; 24:ijms24032923. [PMID: 36769241 PMCID: PMC9917436 DOI: 10.3390/ijms24032923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 02/05/2023] Open
Abstract
Betanidin (Bd) is a nitrogenous metabolite with significant bioactive potential influenced by pH. Its free radical scavenging activity and deprotonation pathway are crucial to studying its physicochemical properties. Motivated by the published discrepancies about the best deprotonation routes in Bd, this work explores all possible pathways for proton extractions on that molecule, by using the direct approach method based on pKa. The complete space of exploration is supported by a linear relation with constant slope, where the pKa is written in terms of the associated deprotonated molecule energy. The deprotonation rounds 1, …, 6 define groups of parallel linear models with constant slope. The intercepts of the models just depend on the protonated energy for each round, and then the pKa can be trivially ordered and explained by the energy. We use the direct approximation method to obtain the value of pKa. We predict all possible outcomes based on a linear model of the energy and some related verified assumptions. We also include a new measure of similarity or dissimilarity between the protonated and deprotonated molecules, via a geometric-chemical descriptor called the Riemann-Mulliken distance (RMD). The RMD considers the cartesian coordinates of the atoms, the atomic mass, and the Mulliken charges. After exploring the complete set of permutations, we show that the successive deprotonation process does not inherit the local energy minimum and that the commutativity of the paths does not hold either. The resulting clusterization of pKa can be explained by the local acid and basic groups of the BD, and the successive deprotonation can be predicted by using the chemical explained linear models, which can avoid unnecessary optimizations. Another part of the research uses our own algorithm based on shape theory to determine the protein's active site automatically, and molecular dynamics confirmed the results of the molecular docking of Bd in protonated and anionic form with the enzyme aldose reductase (AR). Also, we calculate the descriptors associated with the SET and SPLET mechanisms.
Collapse
Affiliation(s)
- Iliana María Ramírez-Velásquez
- Faculty of Exact and Applied Sciences, Instituto Tecnológico Metropolitano, Medellín 050034, Colombia
- Faculty of Basic Sciences, University of Medellin, Medellín 050026, Colombia
- Correspondence: (I.M.R.-V.); (F.J.C.-L.)
| | | | - Ederley Vélez
- Faculty of Basic Sciences, University of Medellin, Medellín 050026, Colombia
| | - Francisco J. Caro-Lopera
- Faculty of Basic Sciences, University of Medellin, Medellín 050026, Colombia
- Correspondence: (I.M.R.-V.); (F.J.C.-L.)
| |
Collapse
|
7
|
The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling. Molecules 2023; 28:molecules28020772. [PMID: 36677828 PMCID: PMC9865902 DOI: 10.3390/molecules28020772] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.
Collapse
|
8
|
Clabbers MT, Martynowycz MW, Hattne J, Gonen T. Hydrogens and hydrogen-bond networks in macromolecular MicroED data. J Struct Biol X 2022; 6:100078. [PMID: 36507068 PMCID: PMC9731847 DOI: 10.1016/j.yjsbx.2022.100078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) is a powerful technique utilizing electron cryo-microscopy (cryo-EM) for protein structure determination of crystalline samples too small for X-ray crystallography. Electrons interact with the electrostatic potential of the sample, which means that the scattered electrons carry information about the charged state of atoms and provide relatively stronger contrast for visualizing hydrogen atoms. Accurately identifying the positions of hydrogen atoms, and by extension the hydrogen bonding networks, is of importance for understanding protein structure and function, in particular for drug discovery. However, identification of individual hydrogen atom positions typically requires atomic resolution data, and has thus far remained elusive for macromolecular MicroED. Recently, we presented the ab initio structure of triclinic hen egg-white lysozyme at 0.87 Å resolution. The corresponding data were recorded under low exposure conditions using an electron-counting detector from thin crystalline lamellae. Here, using these subatomic resolution MicroED data, we identified over a third of all hydrogen atom positions based on strong difference peaks, and directly visualize hydrogen bonding interactions and the charged states of residues. Furthermore, we find that the hydrogen bond lengths are more accurately described by the inter-nuclei distances than the centers of mass of the corresponding electron clouds. We anticipate that MicroED, coupled with ongoing advances in data collection and refinement, can open further avenues for structural biology by uncovering the hydrogen atoms and hydrogen bonding interactions underlying protein structure and function.
Collapse
Affiliation(s)
- Max T.B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Michael W. Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States,Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, United States,Department of Physiology, University of California, Los Angeles, CA 90095, United States,Corresponding author at: Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States.
| |
Collapse
|
9
|
Ajiboye B, Fagbola T, Folorunso I, Salami A, Aletile O, Akomolede B, Ayemoni F, Akinfemiwa K, Anwo V, Ojeleke M, Oyinloye B. In silico identification of chemical compounds in Spondias mombin targeting aldose reductase and glycogen synthase kinase 3β to abate diabetes mellitus. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
10
|
Plapp BV, Gakhar L, Subramanian R. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Acta Crystallogr D Struct Biol 2022; 78:1221-1234. [PMID: 36189742 PMCID: PMC9527765 DOI: 10.1107/s2059798322008361] [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: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022] Open
Abstract
Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD+ and 2,2,2-trifluoroethanol were determined to 1.1-1.3 Å resolution below the `glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 Å2) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 Å2 for the overall complexes and of 5-10 Å2 for C4N of NAD+ and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of ∼0.3 Å and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD+ and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.
Collapse
Affiliation(s)
- Bryce V. Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
| | - Lokesh Gakhar
- Protein and Crystallography Facility, Carver College of Medicine, The University of Iowa, Iowa City, IA 52252, USA
| | - Ramaswamy Subramanian
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
| |
Collapse
|
11
|
Yang Y, He J, Jiang Z, Du X, Chen F, Wang J, Ni H. Characterization of the inhibition of aldose reductase with
p
‐coumaric acid ethyl ester. J Food Biochem 2022; 46:e14370. [DOI: 10.1111/jfbc.14370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Yuanfan Yang
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
| | - Junzhu He
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
| | - Xiping Du
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
| | - Feng Chen
- Department of Food, Nutrition and Packaging Sciences Clemson University Clemson South Carolina USA
| | - Jinling Wang
- School of Forestry Northeast Forestry University Harbin China
| | - Hui Ni
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
| |
Collapse
|
12
|
Anil DA, Aydin BO, Demir Y, Turkmenoglu B. Design, synthesis, biological evaluation and molecular docking studies of novel 1H-1,2,3-Triazole derivatives as potent inhibitors of carbonic anhydrase, acetylcholinesterase and aldose reductase. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132613] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
13
|
Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
Collapse
Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| |
Collapse
|
14
|
Iyamu ID, Vilseck JZ, Yadav R, Noinaj N, Huang R. Exploring Unconventional SAM Analogues To Build Cell-Potent Bisubstrate Inhibitors for Nicotinamide N-Methyltransferase. Angew Chem Int Ed Engl 2022; 61:e202114813. [PMID: 35134268 PMCID: PMC8983580 DOI: 10.1002/anie.202114813] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 12/17/2022]
Abstract
Nicotinamide N-methyltransferase (NNMT) methylates nicotinamide and has been associated with various diseases. Herein, we report the first cell-potent NNMT bisubstrate inhibitor II399, demonstrating a Ki of 5.9 nM in a biochemical assay and a cellular IC50 value of 1.9 μM. The inhibition mechanism and cocrystal structure confirmed II399 engages both the substrate and cofactor binding pockets. Computational modeling and binding data reveal a balancing act between enthalpic and entropic components that lead to II399's low nM binding affinity. Notably, II399 is 1 000-fold more selective for NNMT than closely related methyltransferases. We expect that II399 would serve as a valuable probe to elucidate NNMT biology. Furthermore, this strategy provides the first case of introducing unconventional SAM mimics, which can be adopted to develop cell-potent inhibitors for other SAM-dependent methyltransferases.
Collapse
Affiliation(s)
- Iredia D. Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Ravi Yadav
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, United States
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Institute for Drug Discovery, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
15
|
Rhodanine scaffold: A review of antidiabetic potential and structure-activity relationships (SAR). MEDICINE IN DRUG DISCOVERY 2022. [DOI: 10.1016/j.medidd.2022.100131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
16
|
Balestri F, Moschini R, Mura U, Cappiello M, Del Corso A. In Search of Differential Inhibitors of Aldose Reductase. Biomolecules 2022; 12:biom12040485. [PMID: 35454074 PMCID: PMC9024650 DOI: 10.3390/biom12040485] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
Aldose reductase, classified within the aldo-keto reductase family as AKR1B1, is an NADPH dependent enzyme that catalyzes the reduction of hydrophilic as well as hydrophobic aldehydes. AKR1B1 is the first enzyme of the so-called polyol pathway that allows the conversion of glucose into sorbitol, which in turn is oxidized to fructose by sorbitol dehydrogenase. The activation of the polyol pathway in hyperglycemic conditions is generally accepted as the event that is responsible for a series of long-term complications of diabetes such as retinopathy, cataract, nephropathy and neuropathy. The role of AKR1B1 in the onset of diabetic complications has made this enzyme the target for the development of molecules capable of inhibiting its activity. Virtually all synthesized compounds have so far failed as drugs for the treatment of diabetic complications. This failure may be partly due to the ability of AKR1B1 to reduce alkenals and alkanals, produced in oxidative stress conditions, thus acting as a detoxifying agent. In recent years we have proposed an alternative approach to the inhibition of AKR1B1, suggesting the possibility of a differential inhibition of the enzyme through molecules able to preferentially inhibit the reduction of either hydrophilic or hydrophobic substrates. The rationale and examples of this new generation of aldose reductase differential inhibitors (ARDIs) are presented.
Collapse
Affiliation(s)
- Francesco Balestri
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
| | - Roberta Moschini
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
| | - Umberto Mura
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
| | - Mario Cappiello
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
- Correspondence:
| | - Antonella Del Corso
- Biochemistry Unit, Department of Biology, University of Pisa, Via S. Zeno 51, 56127 Pisa, Italy; (F.B.); (R.M.); (U.M.); (A.D.C.)
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56127 Pisa, Italy
| |
Collapse
|
17
|
Iyamu ID, Vilseck JZ, Yadav R, Noinaj N, Huang R. Exploring Unconventional SAM Analogues To Build Cell‐Potent Bisubstrate Inhibitors for Nicotinamide
N
‐Methyltransferase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Iredia D. Iyamu
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue Institute for Drug Discovery Purdue University Center for Cancer Research Purdue University West Lafayette IN 47907 USA
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology Center for Computational Biology and Bioinformatics Indiana University School of Medicine Indianapolis IN 46202 USA
| | - Ravi Yadav
- Department of Biological Sciences, Markey Center for Structural Biology and the Purdue Institute of Inflammation Immunology and Infectious Disease Purdue University West Lafayette IN 47907 USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology and the Purdue Institute of Inflammation Immunology and Infectious Disease Purdue University West Lafayette IN 47907 USA
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue Institute for Drug Discovery Purdue University Center for Cancer Research Purdue University West Lafayette IN 47907 USA
| |
Collapse
|
18
|
Perspective on the Structural Basis for Human Aldo-Keto Reductase 1B10 Inhibition. Metabolites 2021; 11:metabo11120865. [PMID: 34940623 PMCID: PMC8708191 DOI: 10.3390/metabo11120865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Human aldo-keto reductase 1B10 (AKR1B10) is overexpressed in many cancer types and is involved in chemoresistance. This makes AKR1B10 to be an interesting drug target and thus many enzyme inhibitors have been investigated. High-resolution crystallographic structures of AKR1B10 with various reversible inhibitors were deeply analyzed and compared to those of analogous complexes with aldose reductase (AR). In both enzymes, the active site included an anion-binding pocket and, in some cases, inhibitor binding caused the opening of a transient specificity pocket. Different structural conformers were revealed upon inhibitor binding, emphasizing the importance of the highly variable loops, which participate in the transient opening of additional binding subpockets. Two key differences between AKR1B10 and AR were observed regarding the role of external loops in inhibitor binding. The first corresponded to the alternative conformation of Trp112 (Trp111 in AR). The second difference dealt with loop A mobility, which defined a larger and more loosely packed subpocket in AKR1B10. From this analysis, the general features that a selective AKR1B10 inhibitor should comply with are the following: an anchoring moiety to the anion-binding pocket, keeping Trp112 in its native conformation (AKR1B10-like), and not opening the specificity pocket in AR.
Collapse
|
19
|
Mohd Siddique MU, Thakur A, Shilkar D, Yasmin S, Halakova D, Kovacikova L, Prnova MS, Stefek M, Acevedo O, Dasararaju G, Devadasan V, Mondal SK, Jayaprakash V. Non-carboxylic acid inhibitors of aldose reductase based on N-substituted thiazolidinedione derivatives. Eur J Med Chem 2021; 223:113630. [PMID: 34175538 DOI: 10.1016/j.ejmech.2021.113630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
In search of dually active PPAR-modulators/aldose reductase (ALR2) inhibitors, 16 benzylidene thiazolidinedione derivatives, previously reported as partial PPARγ agonists, together with additional 18 structural congeners, were studied for aldose reductase inhibitory activity. While no compounds had dual property, our efforts led to the identification of promising inhibitors of ALR2. Eight compounds (11, 15-16, 20-24, 30) from the library of 33 compounds were identified as potent and selective inhibitors of ALR2. Compound 21 was the most effective and selective inhibitor with an IC50 value of 0.95 ± 0.11 and 13.52 ± 0.81 μM against ALR2 and aldehyde reductase (ALR1) enzymes, respectively. Molecular docking and dynamics studies were performed to understand inhibitor-enzyme interactions at the molecular level that determine the potency and selectivity. Compound 21 was further subjected to in silico and in vitro studies to evaluate the pharmacokinetic profile. Being less acidic (pKa = 9.8), the compound might have a superior plasma membrane permeability and reach the cytosolic ALR2. This fact together with excellent drug-likeness criteria points to improved bioavailability compared to the clinically used compound Epalrestat. The designed compounds represent a novel group of non-carboxylate inhibitors of aldose reductase with an improved physicochemical profile.
Collapse
Affiliation(s)
- Mohd Usman Mohd Siddique
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India; Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, 424001, (MH), India.
| | - Abhishek Thakur
- Department of Chemistry, University of Miami, Coral Gables, Florida, 33146, USA.
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India.
| | - Sabina Yasmin
- Department of Pharmaceutical Sciences & Technology, Mesra, Ranchi, 835215, (JH), India; Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 61441, Saudi Arabia.
| | - Dominika Halakova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Lucia Kovacikova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Marta Soltesova Prnova
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Milan Stefek
- Institute of Experimental Pharmacology and Toxicology, CEM, Slovak Academy of Sciences, Bratislava, Slovak Republic.
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida, 33146, USA.
| | - Gayathri Dasararaju
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, (TN), India.
| | - Velmurugan Devadasan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, (TN), India.
| | - Susanta Kumar Mondal
- TCG Life Sciences Ltd, Block-EP & GP, BIPL, Tower-B, Saltlake, Sector-V, Kolkata, 700091, (WB), India.
| | | |
Collapse
|
20
|
Rudnev VR, Kulikova LI, Nikolsky KS, Malsagova KA, Kopylov AT, Kaysheva AL. Current Approaches in Supersecondary Structures Investigation. Int J Mol Sci 2021; 22:11879. [PMID: 34769310 PMCID: PMC8584461 DOI: 10.3390/ijms222111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Proteins expressed during the cell cycle determine cell function, topology, and responses to environmental influences. The development and improvement of experimental methods in the field of structural biology provide valuable information about the structure and functions of individual proteins. This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories for storage, as well as methods of molecular dynamics research. The interest in the study of supersecondary structures in proteins is due to their autonomous stability outside the protein globule, which makes it possible to study folding processes, conformational changes in protein isoforms, and aberrant proteins with high productivity.
Collapse
Affiliation(s)
- Vladimir R. Rudnev
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Liudmila I. Kulikova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS—The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Kirill S. Nikolsky
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
| | - Kristina A. Malsagova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
| | - Arthur T. Kopylov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
| | - Anna L. Kaysheva
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (V.R.R.); (L.I.K.); (K.S.N.); (A.T.K.); (A.L.K.)
| |
Collapse
|
21
|
Type 2 Diabetes Mellitus Mediation by the Disruptive Activity of Environmental Toxicants on Sex Hormone Receptors: In Silico Evaluation. TOXICS 2021; 9:toxics9100255. [PMID: 34678951 PMCID: PMC8538912 DOI: 10.3390/toxics9100255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022]
Abstract
This study investigates the disruptive activity of environmental toxicants on sex hormone receptors mediating type 2 diabetes mellitus (T2DM). Toxicokinetics, gene target prediction, molecular docking, molecular dynamics, and gene network analysis were applied in silico techniques. From the results, permethrin, perfluorooctanoic acid, dichlorodiphenyltrichloroethane, O-phenylphenol, bisphenol A, and diethylstilbestrol were the active toxic compounds that could modulate androgen (AR) and estrogen-α and -β receptors (ER) to induce T2DM. Early growth response 1 (EGR1), estrogen receptor 1 (ESR1), and tumour protein 63 (TP63) were the major transcription factors, while mitogen-activated protein kinases (MAPK) and cyclin-dependent kinases (CDK) were the major kinases upregulated by these toxicants via interactions with intermediary proteins such as PTEN, AKT1, NfKβ1, SMAD3 and others in the gene network analysis to mediate T2DM. These toxicants pose a major challenge to public health; hence, monitoring their manufacture, use, and disposal should be enforced. This would ensure reduced interaction between people and these toxic chemicals, thereby reducing the incidence and prevalence of T2DM.
Collapse
|
22
|
González-Álvarez H, Bravo-Jiménez A, Martínez-Arellanes M, Gamboa-Osorio GO, Chávez-Gutiérrez E, González-Hernández LA, Gallardo-Ignacio K, Quintana-Romero OJ, Ariza-Castolo A, Guerra-Araiza C, Martino-Roaro L, Meneses-Ruiz DM, Pinto-Almazán R, Loza-Mejía MA. In Silico-Based Design and In Vivo Evaluation of an Anthranilic Acid Derivative as a Multitarget Drug in a Diet-Induced Metabolic Syndrome Model. Pharmaceuticals (Basel) 2021; 14:914. [PMID: 34577613 PMCID: PMC8466046 DOI: 10.3390/ph14090914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Metabolic syndrome (MetS) is a complex disease that affects almost a quarter of the world's adult population. In MetS, diabetes, obesity, hyperglycemia, high cholesterol, and high blood pressure are the most common disorders. Polypharmacy is the most used strategy for managing conditions related to MetS, but it has drawbacks such as low medication adherence. Multitarget ligands have been proposed as an interesting approach to developing drugs to treat complex diseases. However, suitable preclinical models that allow their evaluation in a context closer to a clinical situation of a complex disease are needed. From molecular docking studies, compound 1b, a 5-aminoanthranilic acid derivative substituted with 4'-trifluoromethylbenzylamino and 3',4'-dimethoxybenzamide moieties, was identified as a potential multitarget drug, as it showed high in silico affinity against targets related to MetS, including PPAR-α, PPAR-γ, and HMG-CoA reductase. It was evaluated in a diet-induced MetS rat model and simultaneously lowered blood pressure, glucose, total cholesterol, and triglyceride levels after a 14-day treatment. No toxicity events were observed during an acute lethal dose evaluation test at 1500 mg/kg. Hence, the diet-induced MetS model is suitable for evaluating treatments for MetS, and compound 1b is an attractive starting point for developing multitarget drugs.
Collapse
Affiliation(s)
- Héctor González-Álvarez
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (H.G.-Á.); (A.B.-J.); (M.M.-A.); (G.O.G.-O.); (L.M.-R.)
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Astrid Bravo-Jiménez
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (H.G.-Á.); (A.B.-J.); (M.M.-A.); (G.O.G.-O.); (L.M.-R.)
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Matilda Martínez-Arellanes
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (H.G.-Á.); (A.B.-J.); (M.M.-A.); (G.O.G.-O.); (L.M.-R.)
| | - Gabriela Odette Gamboa-Osorio
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (H.G.-Á.); (A.B.-J.); (M.M.-A.); (G.O.G.-O.); (L.M.-R.)
| | - Edwin Chávez-Gutiérrez
- Molecular Biology in Metabolic and Neurodegenerative Diseases Laboratory, Research Unit, High Speciality Regional Hospital of Ixtapaluca (HRAEI), Carretera Federal México-Puebla Km 34.5, Ixtapaluca 56530, Mexico; (E.C.-G.); (L.A.G.-H.); (K.G.-I.)
| | - Lino A. González-Hernández
- Molecular Biology in Metabolic and Neurodegenerative Diseases Laboratory, Research Unit, High Speciality Regional Hospital of Ixtapaluca (HRAEI), Carretera Federal México-Puebla Km 34.5, Ixtapaluca 56530, Mexico; (E.C.-G.); (L.A.G.-H.); (K.G.-I.)
| | - Karina Gallardo-Ignacio
- Molecular Biology in Metabolic and Neurodegenerative Diseases Laboratory, Research Unit, High Speciality Regional Hospital of Ixtapaluca (HRAEI), Carretera Federal México-Puebla Km 34.5, Ixtapaluca 56530, Mexico; (E.C.-G.); (L.A.G.-H.); (K.G.-I.)
| | - Osvaldo J. Quintana-Romero
- Department of Chemistry, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (O.J.Q.-R.); (A.A.-C.)
| | - Armando Ariza-Castolo
- Department of Chemistry, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, Mexico City 07360, Mexico; (O.J.Q.-R.); (A.A.-C.)
| | - Christian Guerra-Araiza
- Medical Research Unit in Pharmacology, Specialities Hospital Bernardo Sepúlveda, National Medical Center XXI Century, Social Security Mexican Institute (IMSS), Av. Cuauhtémoc 330, Mexico City 06720, Mexico;
| | - Laura Martino-Roaro
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (H.G.-Á.); (A.B.-J.); (M.M.-A.); (G.O.G.-O.); (L.M.-R.)
- Incarnate Word University Center, Tlacoquemecatl 433, Mexico City 03100, Mexico
| | - Dulce María Meneses-Ruiz
- Noncommunicable Diseases Research Group, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico;
| | - Rodolfo Pinto-Almazán
- Molecular Biology in Metabolic and Neurodegenerative Diseases Laboratory, Research Unit, High Speciality Regional Hospital of Ixtapaluca (HRAEI), Carretera Federal México-Puebla Km 34.5, Ixtapaluca 56530, Mexico; (E.C.-G.); (L.A.G.-H.); (K.G.-I.)
| | - Marco A. Loza-Mejía
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (H.G.-Á.); (A.B.-J.); (M.M.-A.); (G.O.G.-O.); (L.M.-R.)
| |
Collapse
|
23
|
Ajayeoba TA, Woods JO, Ayeni AO, Ajayi TJ, Akeem RA, Hosten EC, Akinyele OF. Synthesis, crystallographic, computational and molecular docking studies of new acetophenone-benzoylhydrazones. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
24
|
Ford MC, Rappé AK, Ho PS. A Reduced Generalized Force Field for Biological Halogen Bonds. J Chem Theory Comput 2021; 17:5369-5378. [PMID: 34232642 DOI: 10.1021/acs.jctc.1c00362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The halogen bond (or X-bond) is a noncovalent interaction that is increasingly recognized as an important design tool for engineering protein-ligand interactions and controlling the structures of proteins and nucleic acids. In the past decade, there have been significant efforts to characterize the structure-energy relationships of this interaction in macromolecules. Progress in the computational modeling of X-bonds in biological molecules, however, has lagged behind these experimental studies, with most molecular mechanics/dynamics-based simulation methods not properly treating the properties of the X-bond. We had previously derived a force field for biological X-bonds (ffBXB) based on a set of potential energy functions that describe the anisotropic electrostatic and shape properties of halogens participating in X-bonds. Although fairly accurate for reproducing the energies within biomolecular systems, including X-bonds engineered into a DNA junction, the ffBXB with its seven variable parameters was considered to be too unwieldy for general applications. In the current study, we have generalized the ffBXB by reducing the number of variables to just one for each halogen type and show that this remaining electrostatic variable can be estimated for any new halogenated molecule through a standard restricted electrostatic potential calculation of atomic charges. In addition, we have generalized the ffBXB for both nucleic acids and proteins. As a proof of principle, we have parameterized this reduced and more general ffBXB against the AMBER force field. The resulting parameter set was shown to accurately recapitulate the quantum mechanical landscape and experimental interaction energies of X-bonds incorporated into DNA junction and T4 lysozyme model systems. Thus, this reduced and generalized ffBXB is more readily adaptable for incorporation into classical molecular mechanics/dynamics algorithms, including those commonly used to design inhibitors against therapeutic targets in medicinal chemistry and materials in biomolecular engineering.
Collapse
Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Anthony K Rappé
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| |
Collapse
|
25
|
Sonowal H, Ramana KV. Development of Aldose Reductase Inhibitors for the Treatment of Inflammatory Disorders and Cancer: Current Drug Design Strategies and Future Directions. Curr Med Chem 2021; 28:3683-3712. [PMID: 33109031 DOI: 10.2174/0929867327666201027152737] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/22/2022]
Abstract
Aldose Reductase (AR) is an enzyme that converts glucose to sorbitol during the polyol pathway of glucose metabolism. AR has been shown to be involved in the development of secondary diabetic complications due to its involvement in causing osmotic as well as oxidative stress. Various AR inhibitors have been tested for their use to treat secondary diabetic complications, such as retinopathy, neuropathy, and nephropathy in clinical studies. Recent studies also suggest the potential role of AR in mediating various inflammatory complications. Therefore, the studies on the development and potential use of AR inhibitors to treat inflammatory complications and cancer besides diabetes are currently on the rise. Further, genetic mutagenesis studies, computer modeling, and molecular dynamics studies have helped design novel and potent AR inhibitors. This review discussed the potential new therapeutic use of AR inhibitors in targeting inflammatory disorders and cancer besides diabetic complications. Further, we summarized studies on how AR inhibitors have been designed and developed for therapeutic purposes in the last few decades.
Collapse
Affiliation(s)
- Himangshu Sonowal
- Moores Cancer Center, University of California San Diego, La Jolla, California 92037, United States
| | - Kota V Ramana
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, United States
| |
Collapse
|
26
|
Efficient Electrocatalytic Approach to Spiro[Furo[3,2-b]pyran-2,5′-pyrimidine] Scaffold as Inhibitor of Aldose Reductase. ELECTROCHEM 2021. [DOI: 10.3390/electrochem2020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A continuously growing interest in convenient and ‘green’ reaction techniques encourages organic chemists to elaborate on new synthetic methodologies. Nowadays, organic electrochemistry is a new useful method with important synthetic and ecological advantages. The employment of an electrocatalytic methodology in cascade reactions is very promising because it provides the combination of the synthetic virtues of the cascade strategy with the ecological benefits and convenience of electrocatalytic procedures. In this research, a new type of the electrocatalytic cascade transformation was found: the electrochemical cyclization of 1,3-dimethyl-5-[[3-hydroxy-6-(hydroxymethyl)-4-oxo-4H-pyran-2-yl](aryl)methyl]pyrimidine-2,4,6(1H,3H,5H)-triones was carried out in alcohols in an undivided cell in the presence of sodium halides with the selective formation of spiro[furo[3,2-b]pyran-2,5′-pyrimidines] in 59-95% yields. This new electrocatalytic process is a selective, facile, and efficient way to create spiro[furo[3,2-b]pyran-2,5′-pyrimidines], which are pharmacologically active heterocyclic systems with different biomedical applications. Spiro[furo[3,2-b]pyran-2,5′-pyrimidines] were found to occupy the binding pocket of aldose reductase and inhibit it. The values of the binding energy and Lead Finder’s Virtual Screening scoring function showed that the formation of protein–ligand complexes was favorable. The synthesized compounds are promising for the inhibition of aldose reductase. This makes them interesting for study in the treatment of diabetes or similar diseases.
Collapse
|
27
|
Sekhon G, Singh B, Singh R. Role of Cys-298 in specific recognition of glutathione by aldose reductase. J Biomol Struct Dyn 2021; 40:6880-6888. [PMID: 33627036 DOI: 10.1080/07391102.2021.1891138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aldose reductase (AR) is an NADPH-dependent oxidoreductase that is well-studied for its role in Diabetes Mellitus. Glutathione conjugated aldehydes are efficiently catalysed by AR. We have employed molecular dynamics simulations to investigate the dynamics of a glutathione analog, γ-glutamyl-S-(1,2-di-carboxyethyl)-cysteinyl-glycine (DCEG), into the binding pocket of AR. Study revealed that backbone nitrogens of Ala-299 and Leu-300 form a tiny pocket gated by thiol group of Cys-298. The glycine moiety of DCEG was able to displace the thiol group of Cys-298 to make hydrogen bond interactions with backbone of Ala-299, Leu-300, and Leu-301. This study provides the details of the dynamic interactions of DCEG in the binding pocket of AR, and shall aid in the design/discovery of differential inhibitors against AR.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Gurprit Sekhon
- Department cum National Centre for Human Genome Studies & Research, Pharmacy Extention Block, Panjab University, Chandigarh, India
| | - Balvinder Singh
- Bioinformatics Center, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ranvir Singh
- Department cum National Centre for Human Genome Studies & Research, Pharmacy Extention Block, Panjab University, Chandigarh, India
| |
Collapse
|
28
|
Abiotic reduction of ketones with silanes catalysed by carbonic anhydrase through an enzymatic zinc hydride. Nat Chem 2021; 13:312-318. [PMID: 33603222 PMCID: PMC8675236 DOI: 10.1038/s41557-020-00633-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Enzymatic reactions through mononuclear metal hydrides are unknown in nature, despite the prevalence of such intermediates in the reactions of synthetic transition-metal catalysts. If metalloenzymes would react through abiotic intermediates like these, then the scope of enzyme-catalyzed reactions would expand. Here we show that zinc-containing carbonic anhydrase enzymes catalyze hydride transfers from silanes to ketones with high enantioselectivity and report mechanistic data providing strong evidence that the process involves a mononuclear zinc hydride. This work shows that abiotic silanes can act as reducing equivalents in an enzyme-catalyzed process and that monomeric hydrides of electropositive metals, which are typically unstable in protic environments, can be catalytic intermediates in enzymatic processes. Overall, this work bridges a gap between the types of transformations in molecular catalysis and biocatalysis.
Collapse
|
29
|
Decato DA, Riel AMS, May JH, Bryantsev VS, Berryman OB. Theoretical, Solid‐State, and Solution Quantification of the Hydrogen Bond‐Enhanced Halogen Bond. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel A. Decato
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
| | - Asia Marie S. Riel
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
| | - James H. May
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
| | | | - Orion B. Berryman
- Department of Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula MT 59812 USA
| |
Collapse
|
30
|
Choudhary S, Silakari O. Virtual screening of epalrestat mimicking selective ALR2 inhibitors from natural product database: auto pharmacophore, ADMET prediction and molecular dynamics approach. J Biomol Struct Dyn 2021; 40:6052-6070. [PMID: 33480327 DOI: 10.1080/07391102.2021.1875878] [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] [Indexed: 01/21/2023]
Abstract
Epalrestat is the only effective aldose reductase (ALR2) inhibitor available in the market for the treatment of diabetic neuropathy. Clinical effectiveness of epalrestat in diabetic neuropathy encouraged us to develop some more ALR2 inhibitors with a better therapeutic profile. Herein, we utilized the pharmacophoric features of epalrestat to search some novel ALR2 inhibitors from an InterBioScreen database of natural compounds. ADME and PAINS filters were applied to provide drug-likeness and to remove toxicophores from the screened hits. The pharmacophoric features of 4-hydroxy-2-nonenal (HNE), a well-known substrate of ALR1, were also explored to identify selective ALR2 inhibitors. The structure-based analysis was then adopted to find out the molecules showing interactions with ALR2 which are crucial for their therapeutic activity. These interaction patterns and binding modes were compared with that of epalrestat. Molecular dynamics (MD) analysis was also carried out to get more insight into the interactions of screened hits in the catalytic domain of ALR2. Additionally, the top hits were docked and simulated with aldehyde reductase (ALR1) to determine their selectivity for ALR2 over ALR1. Overall, five hits including STOCKIN-44771, STOCKIN-46041, STOCKIN-59369, STOCKIN-69620 and STOCKIN-88220 were found to possess a good therapeutic profile in terms of key interactions, binding energies and drug-likeness. Two hits, STOCKIN-46041 and STOCKIN-59369, were identified as the most selective ALR2 inhibitors when assessed their selectivity profile.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shalki Choudhary
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| |
Collapse
|
31
|
Shehzad MT, Imran A, Hameed A, Rashida MA, Bibi M, Uroos M, Asari A, Iftikhar S, Mohamad H, Tahir MN, Shafiq Z, Iqbal J. Exploring synthetic and therapeutic prospects of new thiazoline derivatives as aldose reductase (ALR2) inhibitors. RSC Adv 2021; 11:17259-17282. [PMID: 35479726 PMCID: PMC9033183 DOI: 10.1039/d1ra01716k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
Inhibition of aldose reductase (ALR2) by using small heterocyclic compounds provides a viable approach for the development of new antidiabetic agents. With our ongoing interest towards aldose reductase (ALR2) inhibition, we have synthesized and screened a series of thiazoline derivatives (5a–k, 6a–f, 7a–1 & 8a–j) to find a lead as a potential new antidiabetic agent. The bioactivity results showed the thiazoline-based compound 7b having a benzyl substituent and nitrophenyl substituent-bearing compound 8e were identified as the most potent molecules with IC50 values of 1.39 ± 2.21 μM and 1.52 ± 0.78 μM respectively compared with the reference sorbinil with an IC50 value of 3.14 ± 0.02 μM. Compound 7b with only 23.4% inhibition for ALR1 showed excellent selectivity for the targeted ALR2 to act as a potential lead for the development of new therapeutic agents for diabetic complications. Inhibition of aldose reductase (ALR2) by using small heterocyclic compounds provides a viable approach for the development of new antidiabetic agents.![]()
Collapse
Affiliation(s)
| | - Aqeel Imran
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Abdul Hameed
- Department of Chemistry, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
- Department of Chemistry, University of Sahiwal, Sahiwal, 57000, Pakistan
| | - Mariya al Rashida
- Department of Chemistry, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Marium Bibi
- Department of Biosciences, 90 and 100 Clifton, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Block 5, Clifton, Karachi, 75600, Pakistan
| | - Maliha Uroos
- Institute of Chemistry, University of the Punjab, Lahore, 54590, Pakistan
| | - Asnuzilawati Asari
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Shafia Iftikhar
- Department of Chemistry, University of Sahiwal, Sahiwal, 57000, Pakistan
| | - Habsah Mohamad
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | | | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| |
Collapse
|
32
|
Decato DA, Riel AMS, May JH, Bryantsev VS, Berryman OB. Theoretical, Solid-State, and Solution Quantification of the Hydrogen Bond-Enhanced Halogen Bond. Angew Chem Int Ed Engl 2020; 60:3685-3692. [PMID: 33150716 DOI: 10.1002/anie.202012262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/20/2020] [Indexed: 01/02/2023]
Abstract
Proximal noncovalent forces are commonplace in natural systems and understanding the consequences of their juxtaposition is critical. This paper experimentally quantifies for the first time a Hydrogen Bond-Enhanced Halogen Bond (HBeXB) without the complexities of protein structure or preorganization. An HBeXB is a halogen bond that has been strengthened when the halogen donor simultaneously accepts a hydrogen bond. Our theoretical studies suggest that electron-rich halogen bond donors are strengthened most by an adjacent hydrogen bond. Furthermore, stronger hydrogen bond donors enhance the halogen bond the most. X-ray crystal structures of halide complexes (X- =Br- , I- ) reveal that HBeXBs produce shorter halogen bonds than non-hydrogen bond analogues. 19 F NMR titrations with chloride highlight that the HBeXB analogue exhibits stronger binding. Together, these results form the foundation for future studies concerning hydrogen bonds and halogen bonds in close proximity.
Collapse
Affiliation(s)
- Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Asia Marie S Riel
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - James H May
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | | | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| |
Collapse
|
33
|
Kucerova-Chlupacova M, Halakova D, Majekova M, Treml J, Stefek M, Soltesova Prnova M. (4-Oxo-2-thioxothiazolidin-3-yl)acetic acids as potent and selective aldose reductase inhibitors. Chem Biol Interact 2020; 332:109286. [DOI: 10.1016/j.cbi.2020.109286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022]
|
34
|
Eriksson A, Caldararu O, Ryde U, Oksanen E. Automated orientation of water molecules in neutron crystallographic structures of proteins. Acta Crystallogr D Struct Biol 2020; 76:1025-1032. [PMID: 33021504 DOI: 10.1107/s2059798320011729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/26/2020] [Indexed: 11/10/2022] Open
Abstract
The structure and function of proteins are strongly affected by the surrounding solvent water, for example through hydrogen bonds and the hydrophobic effect. These interactions depend not only on the position, but also on the orientation, of the water molecules around the protein. Therefore, it is often vital to know the detailed orientations of the surrounding ordered water molecules. Such information can be obtained by neutron crystallography. However, it is tedious and time-consuming to determine the correct orientation of every water molecule in a structure (there are typically several hundred of them), which is presently performed by manual evaluation. Here, a method has been developed that reliably automates the orientation of a water molecules in a simple and relatively fast way. Firstly, a quantitative quality measure, the real-space correlation coefficient, was selected, together with a threshold that allows the identification of water molecules that are oriented. Secondly, the refinement procedure was optimized by varying the refinement method and parameters, thus finding settings that yielded the best results in terms of time and performance. It turned out to be favourable to employ only the neutron data and a fixed protein structure when reorienting the water molecules. Thirdly, a method has been developed that identifies and reorients inadequately oriented water molecules systematically and automatically. The method has been tested on three proteins, galectin-3C, rubredoxin and inorganic pyrophosphatase, and it is shown that it yields improved orientations of the water molecules for all three proteins in a shorter time than manual model building. It also led to an increased number of hydrogen bonds involving water molecules for all proteins.
Collapse
Affiliation(s)
- Axl Eriksson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source (ESS) ERIC, PO Box 176, SE-221 00 Lund, Sweden
| |
Collapse
|
35
|
Kousaxidis A, Petrou A, Lavrentaki V, Fesatidou M, Nicolaou I, Geronikaki A. Aldose reductase and protein tyrosine phosphatase 1B inhibitors as a promising therapeutic approach for diabetes mellitus. Eur J Med Chem 2020; 207:112742. [PMID: 32871344 DOI: 10.1016/j.ejmech.2020.112742] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Diabetes mellitus is a metabolic disease characterized by high blood glucose levels and usually associated with several chronic pathologies. Aldose reductase and protein tyrosine phosphatase 1B enzymes have identified as two novel molecular targets associated with the onset and progression of type II diabetes and related comorbidities. Although many inhibitors against these enzymes have already found in the field of diabetic mellitus, the research for discovering more effective and selective agents with optimal pharmacokinetic properties continues. In addition, dual inhibition of these target proteins has proved as a promising therapeutic approach. A variety of diverse scaffolds are presented in this review for the future design of potent and selective inhibitors of aldose reductase and protein tyrosine phosphatase 1B based on the most important structural features of both enzymes. The discovery of novel dual aldose reductase and protein tyrosine phosphatase 1B inhibitors could be effective therapeutic molecules for the treatment of insulin-resistant type II diabetes mellitus. The methods used comprise a literature survey and X-ray crystal structures derived from Protein Databank (PDB). Despite the available therapeutic options for type II diabetes mellitus, the inhibitors of aldose reductase and protein tyrosine phosphatase 1B could be two promising approaches for the effective treatment of hyperglycemia and diabetes-associated pathologies. Due to the poor pharmacokinetic profile and low in vivo efficacy of existing inhibitors of both targets, the research turned to more selective and cell-permeable agents as well as multi-target molecules.
Collapse
Affiliation(s)
- Antonios Kousaxidis
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Anthi Petrou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Vasiliki Lavrentaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Maria Fesatidou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Ioannis Nicolaou
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece
| | - Athina Geronikaki
- School of Health, Department of Pharmacy, Aristotle University of Thessaloniki, 54124, Greece.
| |
Collapse
|
36
|
Exploiting oxadiazole-sulfonamide hybrids as new structural leads to combat diabetic complications via aldose reductase inhibition. Bioorg Chem 2020; 99:103852. [DOI: 10.1016/j.bioorg.2020.103852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/11/2023]
|
37
|
Hayakawa D, Sawada N, Watanabe Y, Gouda H. A molecular interaction field describing nonconventional intermolecular interactions and its application to protein–ligand interaction prediction. J Mol Graph Model 2020; 96:107515. [DOI: 10.1016/j.jmgm.2019.107515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
|
38
|
Arora M, Choudhary S, Singh PK, Sapra B, Silakari O. Structural investigation on the selective COX-2 inhibitors mediated cardiotoxicity: A review. Life Sci 2020; 251:117631. [PMID: 32251635 DOI: 10.1016/j.lfs.2020.117631] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 03/31/2020] [Indexed: 01/30/2023]
Abstract
Initially, the selective COX-2 inhibitors were developed as safer alternatives to the conventional NSAIDs, but later on, most of them were withdrawn from the market due to the risk of heart attack and stroke. Celecoxib, the first selective COX-2 inhibitor, was approved by the Food and Drug Administration (FDA) in December 1998 and was taken back from the market in 2004. Since then, many coxibs have been discontinued one by one due to adverse cardiovascular events. United States (US), Australian and European authorities related to Therapeutic Goods Administration (TGA) implemented the requirements to carry the "Black box" warning on the labels of COX-2 drugs highlighting the risks of serious cardiovascular events. These facts encouraged the researchers to explore them well and find out the biochemical basis behind the cardiotoxicity. From the last few decades, the molecular mechanisms behind the coxibs have regained the attention, especially the specific structural features of the selective COX-2 inhibitors that are associated with cardiotoxicity. This review discusses the key structural features of the selective COX-2 inhibitors and underlying mechanisms that are responsible for the cardiotoxicity. This report also unfolds different strategies that have been reported in the last 10 years to combat the problem of selective COX-2 inhibitors mediated cardiotoxicity.
Collapse
Affiliation(s)
- Mohit Arora
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Shalki Choudhary
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Pankaj Kumar Singh
- Department of Chemistry and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Bharti Sapra
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India
| | - Om Silakari
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab 147002, India.
| |
Collapse
|
39
|
Vyas B, Choudhary S, Singh PK, Kumar M, Verma H, Singh M, Malik AK, Silakari O. Search for non-acidic ALR2 inhibitors: Evaluation of flavones as targeted agents for the management of diabetic complications. Bioorg Chem 2020; 96:103570. [DOI: 10.1016/j.bioorg.2020.103570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/19/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022]
|
40
|
Michalska K, Kowiel M, Bigelow L, Endres M, Gilski M, Jaskolski M, Joachimiak A. 3D domain swapping in the TIM barrel of the α subunit of Streptococcus pneumoniae tryptophan synthase. Acta Crystallogr D Struct Biol 2020; 76:166-175. [PMID: 32038047 PMCID: PMC7008512 DOI: 10.1107/s2059798320000212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 01/08/2020] [Indexed: 02/10/2023] Open
Abstract
Tryptophan synthase catalyzes the last two steps of tryptophan biosynthesis in plants, fungi and bacteria. It consists of two protein chains, designated α and β, encoded by trpA and trpB genes, that function as an αββα complex. Structural and functional features of tryptophan synthase have been extensively studied, explaining the roles of individual residues in the two active sites in catalysis and allosteric regulation. TrpA serves as a model for protein-folding studies. In 1969, Jackson and Yanofsky observed that the typically monomeric TrpA forms a small population of dimers. Dimerization was postulated to take place through an exchange of structural elements of the monomeric chains, a phenomenon later termed 3D domain swapping. The structural details of the TrpA dimer have remained unknown. Here, the crystal structure of the Streptococcus pneumoniae TrpA homodimer is reported, demonstrating 3D domain swapping in a TIM-barrel fold for the first time. The N-terminal domain comprising the H0-S1-H1-S2 elements is exchanged, while the hinge region corresponds to loop L2 linking strand S2 to helix H2'. The structural elements S2 and L2 carry the catalytic residues Glu52 and Asp63. As the S2 element is part of the swapped domain, the architecture of the catalytic apparatus in the dimer is recreated from two protein chains. The homodimer interface overlaps with the α-β interface of the tryptophan synthase αββα heterotetramer, suggesting that the 3D domain-swapped dimer cannot form a complex with the β subunit. In the crystal, the dimers assemble into a decamer comprising two pentameric rings.
Collapse
Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Lance Bigelow
- Midwest Center for Structural Genomics, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Michael Endres
- Midwest Center for Structural Genomics, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miroslaw Gilski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
41
|
Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
Collapse
Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| |
Collapse
|
42
|
Schirò A, Carlon A, Parigi G, Murshudov G, Calderone V, Ravera E, Luchinat C. On the complementarity of X-ray and NMR data. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100019. [PMID: 32647823 PMCID: PMC7337059 DOI: 10.1016/j.yjsbx.2020.100019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/28/2019] [Accepted: 01/02/2020] [Indexed: 12/20/2022]
Abstract
X-ray crystallography and NMR contain complementary information for the structural characterization of biological macromolecules. X-ray diffraction is primarily sensitive to the overall shape of the molecule, whereas NMR is mostly sensitive to the atomic detail. Their combination can therefore provide a stronger justification for the resulting structure. For their combination we have recently proposed REFMAC-NMR, which relies on primary data from both techniques for joint refinement. This possibility raises the compelling question of how far the complementarity can be extended. In this paper, we describe an integrative approach to the refinement with NMR data of four X-ray structures of hen-egg-white lysozyme, solved at atomic resolution in four different crystal forms, and we demonstrate that the outcome critically depends on the crystal form itself, reflecting the sensitivity of NMR to fine details.
Collapse
Affiliation(s)
- Antonio Schirò
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Azzurra Carlon
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Garib Murshudov
- MRC Laboratory for Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK
| | - Vito Calderone
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
43
|
Mandal SK, Guillot B, Munshi P. Electron density based analysis of N–H⋯OC hydrogen bonds and electrostatic interaction energies in high-resolution secondary protein structures: insights from quantum crystallographic approaches. CrystEngComm 2020. [DOI: 10.1039/d0ce00577k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Limiting values of the topological parameters and the electrostatic interaction energies to establish the presence of true N–H⋯OC H-bonds in protein main-chain have been identified using quantitative and qualitative analyses of electron densities.
Collapse
Affiliation(s)
- Suman K. Mandal
- Chemical and Biological Crystallography Laboratory
- Department of Chemistry
- School of Natural Sciences
- Shiv Nadar University
- Dadri
| | - Benoît Guillot
- Laboratoire de Cristallographie
- Institut Jean Barriol
- Université de Lorraine
- Nancy 54000
- France
| | - Parthapratim Munshi
- Chemical and Biological Crystallography Laboratory
- Department of Chemistry
- School of Natural Sciences
- Shiv Nadar University
- Dadri
| |
Collapse
|
44
|
Singh P, Kumar A, Reena, Gupta A, Patil PS, Prabhu S, Garde C. Vibrational spectroscopic characterization, electronic absorption, optical nonlinearity computation and terahertz investigation of (2E) 3-(4-ethoxyphenyl)-1-(3-bromophenyl) prop-2-en-1-one for NLO device fabrication. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.126909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
45
|
Sekhon G, Singh R. Human aldose reductase unfolds through an intermediate. F1000Res 2019; 8:564. [PMID: 31723418 PMCID: PMC6844136 DOI: 10.12688/f1000research.18963.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/22/2019] [Indexed: 11/26/2022] Open
Abstract
Background: Human aldose reductase (hAR) is the first and rate-limiting enzyme of the polyol pathway. For the development of secondary complications of diabetes in chronic hyperglycemic conditions, one of the critical factors is the increased flux of glucose through the polyol pathway. Due to this clinical implication, hAR attracted considerable attention from the drug discovery perspective. In spite of extensive characterization in the context of biochemical and structural aspects, we know very little about the unfolding behavior of hAR. This study reports equilibrium unfolding studies of hAR. Methods: We carried out thermal denaturation and chemical-induced equilibrium unfolding studies of hAR monitored by circular dichroism and fluorescence spectroscopy. Results: Thermal denaturation studies presented a classical picture of two-state unfolding from native to the denatured state. The data was used to derive thermodynamic parameters and study the thermostability of hAR. Chemical induced equilibrium unfolding studies led us to discover an intermediate state, which gets populated at 3.5-4.0 M and 0.7-2.0 M of urea and GuHCl, respectively. Thermodynamic parameters derived from chemical-induced unfolding are in agreement with those obtained from thermal denaturation of hAR. Conclusion: This study revealed that aldose reductase unfolds from native to the unfolded state via an intermediate. Assessment of the thermodynamic stability of native, intermediate, and unfolded states shows that significant energy barriers separate these states, which ensures the cooperativity of unfolding. As hAR functions in cells that are under osmotic and oxidative stress, these
in vitro findings may have implications for its native conformation under the physiological state.
Collapse
Affiliation(s)
- Gurprit Sekhon
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
| | - Ranvir Singh
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
| |
Collapse
|
46
|
Hooshmand SE, Ghadari R, Mohammadian R, Shaabani A, Khavasi HR. Rhodanine‐Furan Bis‐Heterocyclic Frameworks Synthesis via Green One‐Pot Sequential Six‐Component Reactions: A Synthetic and Computational Study. ChemistrySelect 2019. [DOI: 10.1002/slct.201903361] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Seyyed Emad Hooshmand
- Faculty of ChemistryShahid Beheshti University, G. C. P.O. Box 19396–4716 Tehran Iran
| | - Rahim Ghadari
- Department of Organic and BiochemistryFaculty of ChemistryUniversity of Tabriz, Tabriz Iran
| | - Reza Mohammadian
- Faculty of ChemistryShahid Beheshti University, G. C. P.O. Box 19396–4716 Tehran Iran
| | - Ahmad Shaabani
- Faculty of ChemistryShahid Beheshti University, G. C. P.O. Box 19396–4716 Tehran Iran
| | - Hamid Reza Khavasi
- Faculty of ChemistryShahid Beheshti University, G. C. P.O. Box 19396–4716 Tehran Iran
| |
Collapse
|
47
|
Laulumaa S, Kursula P. Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites. Molecules 2019; 24:molecules24173044. [PMID: 31443388 PMCID: PMC6749445 DOI: 10.3390/molecules24173044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 01/28/2023] Open
Abstract
Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C–H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C–H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups, which break planarity rules. For example, in Src homology 3 (SH3) domains, a conserved bent aromatic residue is observed near the ligand binding site. Fatty acid binding protein (FABP) 3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, the deuteration of protein and/or solvent are promising variables in protein crystal optimization.
Collapse
Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
- European Spallation Source, 22100 Lund, Sweden
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.
| |
Collapse
|
48
|
Won Y, Pagar AD, Patil MD, Dawson PE, Yun H. Recent Advances in Enzyme Engineering through Incorporation of Unnatural Amino Acids. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0163-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
49
|
Urzhumtsev AG, Lunin VY. Introduction to crystallographic refinement of macromolecular atomic models. CRYSTALLOGR REV 2019. [DOI: 10.1080/0889311x.2019.1631817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexandre G. Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| |
Collapse
|
50
|
Govindaraj V, Ungati H, Jakka SR, Bose S, Mugesh G. Directing Traffic: Halogen‐Bond‐Mediated Membrane Transport. Chemistry 2019; 25:11180-11192. [DOI: 10.1002/chem.201902243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/15/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Vijayakumar Govindaraj
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Harinarayana Ungati
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Surendar R. Jakka
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Sritama Bose
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| | - Govindasamy Mugesh
- Department of Inorganic & Physical ChemistryIndian Institute of Science Bangalore 560012 India
| |
Collapse
|