fb80b5adabb9c6d05930fe181406c33b ijms-23-07705-v3.pdf 803baeb735d14e06c933fa5fdf17a8e4d2a6099a ijms-23-07705-v3.pdf ce4b7b5731f7abe506951b26fa94a4fa37b8007d7789e1bea1abade5777ee968 ijms-23-07705-v3.pdf Title: Influence of Association on Binding of Disaccharides to YKL-39 and hHyal-1 Enzymes Subject: Disaccharide complexes have been shown experimentally to be useful for drug delivery or as an antifouling surface biofilm, and are promising drug-encapsulation and delivery candidates. Although such complexes are intended for medical applications, to date no studies at the molecular level have been devoted to the influence of complexation on the enzymatic decomposition of polysaccharides. A theoretical approach to this problem has been hampered by the lack of a suitable computational tool for binding such non-covalent complexes to enzymes. Herein, we combine quantum-mechanical calculations of disaccharides complexes with a nonstandard docking GaudiMM engine that can perform such a task. Our results on four different complexes show that they are mostly stabilized by electrostatic interactions and hydrogen bonds. This strong non-covalent stabilization demonstrates the studied complexes are some excellent candidates for self-assembly smart materials, useful for drug encapsulation and delivery. Their advantage lies also in their biocompatible and biodegradable character. Keywords: disaccharides; complexation; docking; DFT; GaudiMM Author: Agnieszka Krzemińska, José-Emilio Sánchez-Aparicio, Jean-Didier Maréchal, Agata Paneth and Piotr Paneth Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Mon Jul 18 14:41:07 2022 CEST ModDate: Mon Jul 18 14:45:32 2022 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 4490762 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- LWJOET+VnURWPalladioL Type 1 Custom yes yes no 10 0 RDKEOC+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 YVYUVL+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 XAMBZE+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 GIFXFT+VnURWPalladioL-Bold Type 1 Custom yes yes no 28 0 IRWHZX+TimesNewRomanPSMT Type 1C WinAnsi yes yes no 46 0 CKUPDE+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 49 0 NETTGI+CMSY10 Type 1 Builtin yes yes no 74 0 DDGXWX+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 85 0 CMPMIZ+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 93 0 OWVLUB+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 97 0 RLHDKV+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 101 0 DDGXWX+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 117 0 CMPMIZ+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 125 0 OWVLUB+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 129 0 RLHDKV+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 133 0 DDGXWX+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 143 0 CMPMIZ+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 151 0 OWVLUB+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 155 0 RLHDKV+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 159 0 DDGXWX+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 175 0 QUQSWX+CambriaMath CID TrueType Identity-H yes yes yes 183 0 CMPMIZ+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 191 0 OWVLUB+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 195 0 RLHDKV+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 199 0 KGOIQJ+CambriaMath TrueType WinAnsi yes yes yes 203 0 DDGXWX+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 212 0 CMPMIZ+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 220 0 OWVLUB+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 224 0 RLHDKV+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 228 0 CHGGKZ+PazoMath-Italic Type 1 Builtin yes yes no 239 0 GIGFZE+CMR10 Type 1 Builtin yes yes no 243 0 WWSFAN+EURM10 Type 1 Builtin yes yes no 247 0 MPUDFL+PazoMath Type 1 Builtin yes yes no 254 0 CMPMIZ+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 265 0 OWVLUB+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 269 0 RLHDKV+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 273 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-07-07 02:39:55 CEST RepresentationInformation: ijms-23-07705-v3.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-07-06 19:06:27 CEST Size: 4490762 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 391 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Item: Title: Results and Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Children: Item: Title: Characterization of Interactions in Polyelectrolyte Complexes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: Binding of Isolated Ligands and CHI/FUR Complex to YKL-39 Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Binding of Isolated Ligands and Complexes HA/CHI, HA/CB, and HP/CB to hHyal-1 Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Computational Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Children: Item: Title: Quantum-Mechanical Calculations Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Protein-Systems Setup and Interaction Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Docking Protocol Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Info: Title: Influence of Association on Binding of Disaccharides to YKL-39 and hHyal-1 Enzymes Author: ぁでのどづびぺにち〠かひぺづねどㅄびにち〬〠おはびラ〭ぅねどぬどは〠こメのっとづぺ〭ぁばちひどっどは〬〠おづちの〭いどつどづひ〠きちひラっとちぬ〬〠ぁでちぴち〠ぐちのづぴと〠ちのつ〠ぐどはぴひ〠ぐちのづぴと Subject: Disaccharide complexes have been shown experimentally to be useful for drug delivery or as an antifouling surface biofilm, and are promising drug-encapsulation and delivery candidates. Although such complexes are intended for medical applications, to date no studies at the molecular level have been devoted to the influence of complexation on the enzymatic decomposition of polysaccharides. A theoretical approach to this problem has been hampered by the lack of a suitable computational tool for binding such non-covalent complexes to enzymes. Herein, we combine quantum-mechanical calculations of disaccharides complexes with a nonstandard docking GaudiMM engine that can perform such a task. Our results on four different complexes show that they are mostly stabilized by electrostatic interactions and hydrogen bonds. This strong non-covalent stabilization demonstrates the studied complexes are some excellent candidates for self-assembly smart materials, useful for drug encapsulation and delivery. Their advantage lies also in their biocompatible and biodegradable character. Keywords: disaccharides; complexation; docking; DFT; GaudiMM Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Mon Jul 18 14:41:07 CEST 2022 ModDate: Mon Jul 18 14:45:32 CEST 2022 ID: 0x691db9cf8942452a9b147e2011b01f17, 0x691db9cf8942452a9b147e2011b01f17 Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: GIGFZE+CMR10 FontSubset: true FirstChar: 40 LastChar: 61 FontDescriptor: FontName: GIGFZE+CMR10 Flags: Symbolic FontBBox: -40, -250, 1009, 750 FontFile: true Font: BaseFont: YVYUVL+URWPalladioL-Roma FontSubset: true FirstChar: 1 LastChar: 233 FontDescriptor: FontName: YVYUVL+URWPalladioL-Roma Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: WWSFAN+EURM10 FontSubset: true FirstChar: 25 LastChar: 33 FontDescriptor: FontName: WWSFAN+EURM10 Flags: Symbolic FontBBox: -32, -243, 1060, 720 FontFile: true Font: BaseFont: XAMBZE+URWPalladioL-Ital FontSubset: true FirstChar: 44 LastChar: 122 FontDescriptor: FontName: XAMBZE+URWPalladioL-Ital Flags: Symbolic FontBBox: -170, -305, 1010, 941 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: LWJOET+VnURWPalladioL FontSubset: true FirstChar: 177 LastChar: 226 FontDescriptor: FontName: LWJOET+VnURWPalladioL Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: NETTGI+CMSY10 FontSubset: true FirstChar: 0 LastChar: 14 FontDescriptor: FontName: NETTGI+CMSY10 Flags: Symbolic FontBBox: -29, -960, 1116, 775 FontFile: true Font: BaseFont: GIFXFT+VnURWPalladioL-Bold FontSubset: true FirstChar: 161 LastChar: 178 FontDescriptor: FontName: GIFXFT+VnURWPalladioL-Bold Flags: Symbolic FontBBox: -152, -301, 1000, 935 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: MPUDFL+PazoMath FontSubset: true FirstChar: 68 LastChar: 68 FontDescriptor: FontName: MPUDFL+PazoMath Flags: Symbolic FontBBox: -40, -283, 878, 946 FontFile: true Font: BaseFont: RDKEOC+URWPalladioL-Bold FontSubset: true FirstChar: 3 LastChar: 180 FontDescriptor: FontName: RDKEOC+URWPalladioL-Bold Flags: Symbolic FontBBox: -152, -301, 1000, 935 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: CHGGKZ+PazoMath-Italic FontSubset: true FirstChar: 100 LastChar: 100 FontDescriptor: FontName: CHGGKZ+PazoMath-Italic Flags: Symbolic FontBBox: -70, -277, 902, 733 FontFile: true Pages: Page: Sequence: 1 Annotations: Annotation: Subtype: Link Rect: 54, 323, 152, 332 Annotation: Subtype: Link Rect: 34, 311, 77, 320 Annotation: Subtype: Link Rect: 34, 164, 96, 186 Annotation: Subtype: Link Rect: 126, 90, 154, 99 Annotation: Subtype: Link Rect: 34, 78, 147, 87 Annotation: Subtype: Link Rect: 34, 756, 180, 792 Annotation: Subtype: Link Rect: 515, 756, 560, 792 Annotation: Subtype: Link Rect: 147, 660, 158, 674 Annotation: Subtype: Link Rect: 303, 660, 314, 674 Annotation: Subtype: Link Rect: 429, 660, 440, 674 Annotation: Subtype: Link Rect: 510, 660, 521, 674 Annotation: Subtype: Link Rect: 124, 650, 135, 661 Annotation: Subtype: Link Rect: 443, 246, 450, 255 ActionDest: 279 Annotation: Subtype: Link Rect: 139, 17, 278, 28 Annotation: Subtype: Link Rect: 422, 17, 560, 28 Annotation: Subtype: Link Rect: 34, 408, 87, 427 Page: Sequence: 2 Annotations: Annotation: Subtype: Link Rect: 451, 673, 458, 682 ActionDest: 279 Annotation: Subtype: Link Rect: 310, 585, 317, 594 ActionDest: 279 Annotation: Subtype: Link Rect: 243, 560, 250, 569 ActionDest: 279 Annotation: Subtype: Link Rect: 308, 547, 315, 556 ActionDest: 283 Annotation: Subtype: Link Rect: 398, 334, 405, 343 ActionDest: 283 Annotation: Subtype: Link Rect: 510, 309, 517, 318 ActionDest: 283 Page: Sequence: 3 Annotations: Annotation: Subtype: Link Rect: 327, 736, 334, 744 ActionDest: 283 Annotation: Subtype: Link Rect: 337, 735, 344, 744 ActionDest: 283 Annotation: Subtype: Link Rect: 433, 720, 440, 732 ActionDest: 71 Annotation: Subtype: Link Rect: 504, 501, 516, 510 ActionDest: 283 Annotation: Subtype: Link Rect: 544, 463, 556, 472 ActionDest: 283 Annotation: Subtype: Link Rect: 254, 423, 261, 435 ActionDest: 78 Annotation: Subtype: Link Rect: 426, 260, 433, 272 ActionDest: 78 Page: Sequence: 4 Annotations: Annotation: Subtype: Link Rect: 359, 110, 371, 119 ActionDest: 283 Page: Sequence: 5 Annotations: Annotation: Subtype: Link Rect: 452, 710, 464, 719 ActionDest: 283 Annotation: Subtype: Link Rect: 534, 582, 540, 594 ActionDest: 110 Annotation: Subtype: Link Rect: 191, 570, 198, 582 ActionDest: 107 Annotation: Subtype: Link Rect: 533, 381, 540, 393 ActionDest: 110 Annotation: Subtype: Link Rect: 521, 144, 528, 156 ActionDest: 110 Annotation: Subtype: Link Rect: 194, 132, 201, 144 ActionDest: 167 Page: Sequence: 6 Page: Sequence: 7 Page: Sequence: 8 Annotations: Annotation: Subtype: Link Rect: 391, 607, 398, 621 ActionDest: 110 Annotation: Subtype: Link Rect: 227, 195, 239, 204 ActionDest: 283 Annotation: Subtype: Link Rect: 297, 195, 309, 204 ActionDest: 283 Annotation: Subtype: Link Rect: 462, 195, 474, 204 ActionDest: 283 Annotation: Subtype: Link Rect: 383, 182, 395, 192 ActionDest: 283 Page: Sequence: 9 Annotations: Annotation: Subtype: Link Rect: 493, 633, 505, 642 ActionDest: 283 Annotation: Subtype: Link Rect: 408, 621, 420, 630 ActionDest: 283 Annotation: Subtype: Link Rect: 275, 570, 287, 579 ActionDest: 283 Annotation: Subtype: Link Rect: 338, 570, 350, 579 ActionDest: 283 Annotation: Subtype: Link Rect: 330, 557, 342, 567 ActionDest: 283 Annotation: Subtype: Link Rect: 269, 533, 281, 541 ActionDest: 283 Annotation: Subtype: Link Rect: 339, 533, 351, 541 ActionDest: 283 Annotation: Subtype: Link Rect: 232, 444, 244, 454 ActionDest: 283 Annotation: Subtype: Link Rect: 312, 445, 324, 454 ActionDest: 283 Annotation: Subtype: Link Rect: 284, 344, 296, 353 ActionDest: 283 Annotation: Subtype: Link Rect: 297, 344, 308, 353 ActionDest: 283 Annotation: Subtype: Link Rect: 430, 332, 442, 341 ActionDest: 283 Annotation: Subtype: Link Rect: 208, 172, 215, 181 ActionDest: 283 Page: Sequence: 10 Annotations: Annotation: Subtype: Link Rect: 239, 723, 251, 732 ActionDest: 283 Annotation: Subtype: Link Rect: 243, 698, 255, 707 ActionDest: 283 Annotation: Subtype: Link Rect: 461, 570, 468, 582 ActionDest: 258 Annotation: Subtype: Link Rect: 514, 535, 526, 544 ActionDest: 283 Page: Sequence: 11 Annotations: Annotation: Subtype: Link Rect: 416, 698, 428, 707 ActionDest: 283 Annotation: Subtype: Link Rect: 479, 370, 560, 381 Annotation: Subtype: Link Rect: 165, 359, 294, 369 Annotation: Subtype: Link Rect: 367, 131, 404, 142 Annotation: Subtype: Link Rect: 411, 131, 447, 142 Annotation: Subtype: Link Rect: 410, 108, 447, 119 Annotation: Subtype: Link Rect: 203, 85, 240, 96 Annotation: Subtype: Link Rect: 246, 85, 282, 96 Page: Sequence: 12 Annotations: Annotation: Subtype: Link Rect: 261, 710, 298, 721 Annotation: Subtype: Link Rect: 287, 687, 325, 698 Annotation: Subtype: Link Rect: 293, 664, 330, 675 Annotation: Subtype: Link Rect: 131, 642, 168, 652 Annotation: Subtype: Link Rect: 225, 618, 262, 629 Annotation: Subtype: Link Rect: 416, 606, 453, 617 Annotation: Subtype: Link Rect: 270, 583, 307, 594 Annotation: Subtype: Link Rect: 144, 550, 182, 560 Annotation: Subtype: Link Rect: 492, 526, 529, 537 Annotation: Subtype: Link Rect: 237, 503, 275, 514 Annotation: Subtype: Link Rect: 376, 480, 414, 491 Annotation: Subtype: Link Rect: 257, 434, 294, 445 Annotation: Subtype: Link Rect: 395, 411, 433, 422 Annotation: Subtype: Link Rect: 520, 388, 557, 399 Annotation: Subtype: Link Rect: 246, 365, 283, 376 Annotation: Subtype: Link Rect: 329, 342, 366, 353 Annotation: Subtype: Link Rect: 166, 297, 203, 307 Annotation: Subtype: Link Rect: 220, 274, 257, 284 Annotation: Subtype: Link Rect: 140, 251, 177, 261 Annotation: Subtype: Link Rect: 304, 192, 342, 203 Annotation: Subtype: Link Rect: 337, 169, 374, 180 Annotation: Subtype: Link Rect: 354, 146, 392, 157 Annotation: Subtype: Link Rect: 59, 124, 96, 134 Checksum: 8343f51e Type: CRC32 Checksum: fb80b5adabb9c6d05930fe181406c33b Type: MD5 Checksum: 803baeb735d14e06c933fa5fdf17a8e4d2a6099a Type: SHA-1