1
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Jestilä JS, Wu N, Priante F, Foster AS. Accelerated Lignocellulosic Molecule Adsorption Structure Determination. J Chem Theory Comput 2024; 20:2297-2312. [PMID: 38408381 PMCID: PMC10939001 DOI: 10.1021/acs.jctc.3c01292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024]
Abstract
Here, we present a study combining Bayesian optimization structural inference with the machine learning interatomic potential Neural Equivariant Interatomic Potential (NequIP) to accelerate and enable the study of the adsorption of the conformationally flexible lignocellulosic molecules β-d-xylose and 1,4-β-d-xylotetraose on a copper surface. The number of structure evaluations needed to map out the relevant potential energy surfaces are reduced by Bayesian optimization, while NequIP minimizes the time spent on each evaluation, ultimately resulting in cost-efficient and reliable sampling of large systems and configurational spaces. Although the applicability of Bayesian optimization for the conformational analysis of the more flexible xylotetraose molecule is restricted by the sample complexity bottleneck, the latter can be effectively bypassed with external conformer search tools, such as the Conformer-Rotamer Ensemble Sampling Tool, facilitating the subsequent lower-dimensional global minimum adsorption structure determination. Finally, we demonstrate the applicability of the described approach to find adsorption structures practically equivalent to the density functional theory counterparts at a fraction of the computational cost.
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Affiliation(s)
- Joakim S. Jestilä
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Nian Wu
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Fabio Priante
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Adam S. Foster
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, 920-1192 Kanazawa, Japan
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2
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Folmsbee D, Koes DR, Hutchison GR. Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences. J Chem Inf Model 2023; 63:7401-7411. [PMID: 38000780 PMCID: PMC10716907 DOI: 10.1021/acs.jcim.3c01278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
We performed exhaustive torsion sampling on more than 3 million compounds using the GFN2-xTB method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that must be stable, synthetically accessible, and able to be crystallized. In this work, we evaluate the differences in torsional preferences of experimental crystallographic geometries and gas-phase computed conformers from a broad selection of compounds to determine whether torsional angle distributions obtained from semiempirical methods are suitable priors for conformer sampling. We find that differences in torsion preferences can be mostly attributed to a lack of available experimental crystallographic data with small deviations derived from gas-phase geometry differences. GFN2 demonstrates the ability to provide accurate and reliable torsional preferences that can provide a basis for new methods free from the limitations of experimental data collection. We provide Gaussian-based fits and sampling distributions suitable for torsion sampling and propose an alternative to the widely used "experimental torsion and knowledge distance geometry" (ETKDG) method using quantum torsion-derived distance geometry (QTDG) methods.
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Affiliation(s)
- Dakota
L. Folmsbee
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Department
of Anesthesiology & Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - David R. Koes
- Department
of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Geoffrey R. Hutchison
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemical & Petroleum Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, Pennsylvania 15261, United States
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3
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Hostachy S, Wang H, Zong G, Franke K, Riley AM, Schmieder P, Potter BVL, Shears SB, Fiedler D. Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry 2023; 29:e202302426. [PMID: 37773020 PMCID: PMC7615343 DOI: 10.1002/chem.202302426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Inositol pyrophosphates (PP-IPs) are densely phosphorylated messenger molecules involved in numerous biological processes. PP-IPs contain one or two pyrophosphate group(s) attached to a phosphorylated myo-inositol ring. 5PP-IP5 is the most abundant PP-IP in human cells. To investigate the function and regulation by PP-IPs in biological contexts, metabolically stable analogs have been developed. Here, we report the synthesis of a new fluorinated phosphoramidite reagent and its application for the synthesis of a difluoromethylene bisphosphonate analog of 5PP-IP5 . Subsequently, the properties of all currently reported analogs were benchmarked using a number of biophysical and biochemical methods, including co-crystallization, ITC, kinase activity assays and chromatography. Together, the results showcase how small structural alterations of the analogs can have notable effects on their properties in a biochemical setting and will guide in the choice of the most suitable analog(s) for future investigations.
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Affiliation(s)
- Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Huanchen Wang
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Guangning Zong
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Katy Franke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Andrew M. Riley
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Stephen B. Shears
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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4
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Micheli L, Rajamoni J, Di Cesare Mannelli L, Rajagopalan P, Ghelardini C, Rajagopalan R. DDD-028: A potent, neuroprotective, non-opioid compound for the treatment of diabetic neuropathy. Bioorg Med Chem Lett 2023; 95:129472. [PMID: 37690597 DOI: 10.1016/j.bmcl.2023.129472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Diabetic neuropathy (DN) is a painful, chronic ailment that affects a large segment of diabetic population worldwide. Current medications such as pregabalin or duloxetine treat only the pain symptom associated with DN, but not the underlying nerve damage. DDD-028 (1) is a small molecule that displays potent pain-relieving activity in streptozotocin (STZ)-induced rodent model of DN. Combined with other studies indicating that DDD-028 suppresses astrogliosis and nerve damage induced by the anti-cancer drug, paclitaxel, the present study suggests that DDD-028 would be useful as a disease modifying therapeutic in the treatment of DN. The 3-dimensional structure of DDD-028 was confirmed by single crystal X-ray crystallography.
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Affiliation(s)
- Laura Micheli
- Department of Neuroscience, Psychology, Drug Research and Child Health, NEUROFARBA-Pharmacology and Toxicology Section, University of Florence, Florence, Viale Pieraccini 6, 50139 Florence, Italy
| | - Jagan Rajamoni
- Department of Chemistry and Biochemistry, University of Missouri, St. Louis, One University Blvd., St. Louis, MO 63121, USA
| | - Lorenzo Di Cesare Mannelli
- Department of Neuroscience, Psychology, Drug Research and Child Health, NEUROFARBA-Pharmacology and Toxicology Section, University of Florence, Florence, Viale Pieraccini 6, 50139 Florence, Italy
| | | | - Carla Ghelardini
- Department of Neuroscience, Psychology, Drug Research and Child Health, NEUROFARBA-Pharmacology and Toxicology Section, University of Florence, Florence, Viale Pieraccini 6, 50139 Florence, Italy
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5
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Charvati E, Sun H. Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules. J Phys Chem A 2023; 127:2646-2663. [PMID: 36893434 DOI: 10.1021/acs.jpca.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R2) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.
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Affiliation(s)
- Evangelia Charvati
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Chernykh AV, Kudryk OV, Olifir OS, Dobrydnev AV, Rusanov E, Moskvina VS, Volochnyuk DM, Grygorenko OO. Expanding the Chemical Space of 1,2-Difunctionalized Cyclobutanes. J Org Chem 2023. [PMID: 36780233 DOI: 10.1021/acs.joc.2c02892] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
An efficient approach to the synthesis of previously unavailable or hardly accessible 1,2-difunctionalized cyclobutanes (mostly with NH2/NHBoc, OH, SH, or SO2F groups attached to the carbocycle either directly or via a CH2 unit) relying on the divergent strategy is described. This class of compounds provides sp3-enriched and conformationally restricted building blocks that are of special demand for medicinal chemistry. The target compounds were prepared not only as pure racemic (±)-cis- and (±)-trans-diastereomers but in some cases also as single enantiomers. The developed procedures are readily scaled up and allow obtaining the target compounds on an up to hundred-gram scale. On the basis of the results of 20 X-ray diffraction experiments, structural characterization of the 1,2-difunctionalized cyclobutane core was performed using the extended Cremer-Pople puckering parameters and exit vector (EVP) plots.
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Affiliation(s)
- Anton V Chernykh
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyïv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Oleksandr V Kudryk
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyïv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Oleksandr S Olifir
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyïv 02094, Ukraine.,V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry at National Academy of Sciences of Ukraine, Akademik Kukhar Street 1, Kyïv 02094, Ukraine
| | - Alexey V Dobrydnev
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyïv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
| | - Eduard Rusanov
- Institute of Organic Chemistry at National Academy of Sciences of Ukraine, Akademik Kukhar Street 5, Kyïv 02094, Ukraine.,Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zürich 8093, Switzerland
| | - Viktoriia S Moskvina
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine.,V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry at National Academy of Sciences of Ukraine, Akademik Kukhar Street 1, Kyïv 02094, Ukraine
| | - Dmitriy M Volochnyuk
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyïv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine.,Institute of Organic Chemistry at National Academy of Sciences of Ukraine, Akademik Kukhar Street 5, Kyïv 02094, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd. (www.enamine.net), Chervonotkatska Street 78, Kyïv 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyïv 01601, Ukraine
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7
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Martínez-Haya B, Avilés-Moreno JR, Gámez F, Martens J, Oomens J, Berden G. A Dynamic Proton Bond: MH +·H 2O ⇌ M·H 3O + Interconversion in Loosely Coordinated Environments. J Phys Chem Lett 2023; 14:1294-1300. [PMID: 36723385 PMCID: PMC9923742 DOI: 10.1021/acs.jpclett.2c03832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The interaction of organic molecules with oxonium cations within their solvation shell may lead to the emergence of dynamic supramolecular structures with recurrently changing host-guest chemical identity. We illustrate this phenomenon in benchmark proton-bonded complexes of water with polyether macrocyles. Despite the smaller proton affinity of water versus the ether group, water in fact retains the proton in the form of H3O+, with increasing stability as the coordination number increases. Hindrance in many-fold coordination induces dynamic reversible (ether)·H3O+ ⇌ (etherH+)·H2O interconversion. We perform infrared action ion spectroscopy over a broad spectral range to expose the vibrational signatures of the loose proton bonding in these systems. Remarkably, characteristic bands for the two limiting proton bonding configurations are observed in the experimental vibrational spectra, superimposed onto diffuse bands associated with proton delocalization. These features cannot be described by static equilibrium structures but are accurately modeled within the framework of ab initio molecular dynamics.
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Affiliation(s)
- Bruno Martínez-Haya
- Department
of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | | | - Francisco Gámez
- Departamento
de Química Física, Universidad Complutense, 28040 Madrid, Spain
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
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8
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Ndlangamandla NG, Clayton HS. The crystal structure of trans-dichlorido-(ethylenediamine- κ
2
N, N′)-bis(triphenylphosphine- κ
1
P)ruthenium(II), C 38H 38Cl 2N 2P 2Ru. Z KRIST-NEW CRYST ST 2022. [DOI: 10.1515/ncrs-2022-0448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
C38H38Cl2N2P2Ru, monoclinic, P21/c (no. 14), a = 10.8827(3) Å, b = 30.6226(7) Å, c = 20.2089(4) Å, β = 93.8560(10)°, V = 6719.5(3) Å3, Z = 8, Rgt
(F) = 0.0306, wRref
(F
2) = 0.0636, T = 173(2) K.
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Affiliation(s)
- Nqobile G. Ndlangamandla
- Chemistry Department , University of South Africa , Unisa Science Campus , Johannesburg , South Africa
| | - Hadley S. Clayton
- Chemistry Department , University of South Africa , Unisa Science Campus , Johannesburg , South Africa
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9
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Lalithamaheswari B, Anu Radha C. Structural and conformational dynamics of human milk oligosaccharides, lacto- N-fucopentaose I and II, through molecular dynamics simulation. J Carbohydr Chem 2022. [DOI: 10.1080/07328303.2022.2150203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- B. Lalithamaheswari
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C. Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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10
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Das G, Harikrishna S, Gore KR. Influence of Sugar Modifications on the Nucleoside Conformation and Oligonucleotide Stability: A Critical Review. CHEM REC 2022; 22:e202200174. [PMID: 36048010 DOI: 10.1002/tcr.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Indexed: 12/15/2022]
Abstract
Ribofuranose sugar conformation plays an important role in the structure and dynamics of functional nucleic acids such as siRNAs, AONs, aptamers, miRNAs, etc. To improve their therapeutic potential, several chemical modifications have been introduced into the sugar moiety over the years. The stability of the oligonucleotide duplexes as well as the formation of stable and functional protein-oligonucleotide complexes are dictated by the conformation and dynamics of the sugar moiety. In this review, we systematically categorise various ribofuranose sugar modifications employed in DNAs and RNAs so far. We discuss different stereoelectronic effects imparted by different substituents on the sugar ring and how these effects control sugar puckering. Using this data, it would be possible to predict the precise use of chemical modifications and design novel sugar-modified nucleosides for therapeutic oligonucleotides that can improve their physicochemical properties.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal-721302, India
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11
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Fukunishi Y, Higo J, Kasahara K. Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles. Biophys Rev 2022; 14:1423-1447. [PMID: 36465086 PMCID: PMC9703445 DOI: 10.1007/s12551-022-01015-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/06/2022] [Indexed: 11/29/2022] Open
Abstract
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.
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Affiliation(s)
- Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo 650-0047 Japan ,Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
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12
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Tapala KC, Clayton HS. Crystal structure of propane-1,3-diylbis(diphenylphosphine sulfide) ethanol solvate, C 27H 26P 2S 2. Z KRIST-NEW CRYST ST 2022. [DOI: 10.1515/ncrs-2022-0496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
C27H26P2S2, tetragonal, I4 (no. 79), a = 16.9196(12) Å, c = 9.4187(8) Å, V = 2696.3(4) Å3, Z = 4, R
gt(F) = 0.0341, wR
ref(F
2) = 0.0726, T = 173(2) K.
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Affiliation(s)
- Kgaugelo C. Tapala
- Chemistry Department , University of South Africa , Unisa Science Campus , Johannesburg , 1709 , South Africa
| | - Hadley S. Clayton
- Chemistry Department , University of South Africa , Unisa Science Campus , Johannesburg , 1709 , South Africa
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13
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Panda DP, Swain D, Sundaresan A. Zero-Dimensional (Piperidinium) 2MnBr 4: Ring Puckering-Induced Isostructural Transition and Strong Electron-Phonon Coupling-Mediated Self-Trapped Exciton Emission. Inorg Chem 2022; 61:11377-11386. [PMID: 35820065 DOI: 10.1021/acs.inorgchem.2c01601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report on the synthesis, structure, and photophysical properties of a lead-free organic-inorganic hybrid halide, (Piperidinium)2MnBr4 (PipMBr). It crystallizes in a monoclinic P21/n structure, with isolated MnBr4 tetrahedra representing a zero-dimensional compound. It undergoes a reversible isostructural transition at 422/417 K in the heating/cooling cycle owing to the hydrogen-bonding rearrangement mediated by ring puckering of piperidinium cations. This compound exhibits green emission with a photoluminescence quantum yield of 51%. Interestingly, strong electron-longitudinal optical phonon coupling with γLO of 237 meV is evidenced from the broadening of the temperature-dependent emission linewidth and the Raman spectrum. Such strong electron-phonon coupling and a relatively low Debye temperature (137 K) suggest the self-trapped exciton emission in this compound.
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Affiliation(s)
- Debendra Prasad Panda
- School of Advanced Materials, and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Diptikanta Swain
- Institute of Chemical Technology-IndianOil Odisha Campus, Bhubaneswar 751013, India
| | - A Sundaresan
- School of Advanced Materials, and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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14
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Gorges J, Grimme S, Hansen A, Pracht P. Towards understanding solvation effects on the conformational entropy of non-rigid molecules. Phys Chem Chem Phys 2022; 24:12249-12259. [PMID: 35543018 DOI: 10.1039/d1cp05805c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The absolute molecular entropy is a fundamental quantity for the accurate description of thermodynamic properties. For non-rigid molecules, a substantial part of the entropy can be attributed to a conformational contribution. Systems and properties where this is relevant, e.g., protein-ligand binding affinities or pKa values refer usually to the liquid phase. In this work, the influence of solvation on the conformational entropy is investigated. A recently introduced state-of-the-art and automated computational protocol for the computation of conformational entropies [Pracht et al., Chem. Sci., 2021, 12, 6551-6568.] is applied in combination with fast and accurate semiempirical quantum-chemical methods and implicit solvation models for a set of 25 commercially available drug molecules and five transition metal compounds. Computed gas-phase conformational entropies are compared with values obtained in implicit n-hexane and water. It is found that implicit solvation can have a substantial effect of several cal mol-1 K-1 on the entropy as a result of large conformational changes in the different phases. We conclude that for flexible molecules chemical accuracy for free energies in solution can only be achieved if solvation effects on the conformational ensemble are considered.
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Affiliation(s)
- Johannes Gorges
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Philipp Pracht
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany.
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15
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Schneider AL, Albrecht AV, Huang K, Germann MW, Poon GMK. Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields. Life (Basel) 2022; 12:life12050666. [PMID: 35629334 PMCID: PMC9143812 DOI: 10.3390/life12050666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/22/2022] Open
Abstract
Fixed-charge (non-polarizable) forcefields are accurate and computationally efficient tools for modeling the molecular dynamics of nucleic acid polymers, particularly DNA, well into the µs timescale. The continued utility of these forcefields depends in part on expanding the residue set in step with advancing nucleic acid chemistry and biology. A key step in parameterizing new residues is charge derivation which is self-consistent with the existing residues. As atomic charges are derived by fitting against molecular electrostatic potentials, appropriate structural models are critical. Benchmarking against the existing charge set used in current AMBER nucleic acid forcefields, we report that quantum mechanical models of deoxynucleosides, even at a high level of theory, are not optimal structures for charge derivation. Instead, structures from molecular mechanics minimization yield charges with up to 6-fold lower RMS deviation from the published values, due to the choice of such an approach in the derivation of the original charge set. We present a contemporary protocol for rendering self-consistent charges as well as optimized charges for a panel of nine non-canonical residues that will permit comparison with literature as well as studying the dynamics of novel DNA polymers.
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Affiliation(s)
- Amelia L. Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Amanda V. Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
| | - Gregory M. K. Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (A.L.S.); (A.V.A.); (K.H.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.W.G.); (G.M.K.P.)
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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Impact of Deuteration and Temperature on Furan Ring Dynamics. MOLECULES (BASEL, SWITZERLAND) 2021; 26:molecules26102889. [PMID: 34068118 PMCID: PMC8152745 DOI: 10.3390/molecules26102889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/28/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022]
Abstract
Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.
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Chan L, Morris GM, Hutchison GR. Understanding Conformational Entropy in Small Molecules. J Chem Theory Comput 2021; 17:2099-2106. [DOI: 10.1021/acs.jctc.0c01213] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lucian Chan
- Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, U.K
| | - Garrett M. Morris
- Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford OX1 3LB, U.K
| | - Geoffrey R. Hutchison
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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