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Xiong F, Xu H, Yu M, Chen X, Zhong Z, Guo Y, Chen M, Ou H, Wu J, Xie A, Xiong J, Xu L, Zhang L, Zhong Q, Huang L, Li Z, Zhang T, Jin F, He X. 3CLpro inhibitors: DEL-based molecular generation. Front Pharmacol 2022; 13:1085665. [PMID: 36569316 PMCID: PMC9768338 DOI: 10.3389/fphar.2022.1085665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Molecular generation (MG) via machine learning (ML) has speeded drug structural optimization, especially for targets with a large amount of reported bioactivity data. However, molecular generation for structural optimization is often powerless for new targets. DNA-encoded library (DEL) can generate systematic, target-specific activity data, including novel targets with few or unknown activity data. Therefore, this study aims to overcome the limitation of molecular generation in the structural optimization for the new target. Firstly, we generated molecules using the structure-affinity data (2.96 million samples) for 3C-like protease (3CLpro) from our own-built DEL platform to get rid of using public databases (e.g., CHEMBL and ZINC). Subsequently, to analyze the effect of transfer learning on the positive rate of the molecule generation model, molecular docking and affinity model based on DEL data were applied to explore the enhanced impact of transfer learning on molecule generation. In addition, the generated molecules are subjected to multiple filtering, including physicochemical properties, drug-like properties, and pharmacophore evaluation, molecular docking to determine the molecules for further study and verified by molecular dynamics simulation.
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Affiliation(s)
- Feng Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China,*Correspondence: Feng Xiong, ; Feng Jin, ; Xun He,
| | - Honggui Xu
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Mingao Yu
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Xingyu Chen
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Zhenmin Zhong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Yuhan Guo
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Meihong Chen
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Huanfang Ou
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Jiaqi Wu
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Anhua Xie
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Jiaqi Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Linlin Xu
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Lanmei Zhang
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Qijian Zhong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Liye Huang
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Zhenwei Li
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | | | - Feng Jin
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China,*Correspondence: Feng Xiong, ; Feng Jin, ; Xun He,
| | - Xun He
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China,*Correspondence: Feng Xiong, ; Feng Jin, ; Xun He,
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Chocholousová J, Feig M. Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J Phys Chem B 2007; 110:17240-51. [PMID: 16928023 DOI: 10.1021/jp0627675] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Differences in conformational sampling of DNA with two sets of atomic radii that are used to define the dielectric interface between the solute and the continuum dielectric model of the solvent are investigated. Results suggest that depending on the choice of atomic radii agreement is either closer to experimental data or to explicit solvent simulations. Furthermore, partial conformational transitions toward A-DNA conformations when salt is added within the implicit solvent framework are observed.
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Affiliation(s)
- Jana Chocholousová
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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Abstract
Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo, Prague, Czech Republic
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Burda JV, Shukla MK, Leszczynski J. Theoretical model of the aqua-copper [Cu(H2O)5]+cation interactions with guanine. J Mol Model 2005; 11:362-9. [PMID: 15928918 DOI: 10.1007/s00894-005-0269-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2004] [Accepted: 01/31/2005] [Indexed: 10/25/2022]
Abstract
Pentaaqua complexes of Cu(I) with guanine were optimized at the DFT B3PW91/6-31G(d) level. For the most stable structures, vibration frequencies and NBO charges were computed followed by energy analyses. The order of individual conformers was very sensitive to the method and basis sets used for the calculation. Several conformers are practically degenerated in energy. The inclusion of an entropy term changes the order of the conformers' stability. Water molecules associated at the N9 position of guanine are favored by the inclusion of the entropy correction. Bonding energies of Cu-O(aqua) interactions were estimated to be about 60 kcal mol(-1) and for Cu-N7 bonding in the range of 75-83 kcal mol(-1). The broad range in Cu-N interaction energies demonstrates the role of induction effects caused by water molecules associated at the various sites of guanine. The charge distribution of the guanine molecule is changed remarkably by the coordination of a Cu(I) cation, which can also change the base-pairing pattern of the guanine.
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Affiliation(s)
- Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.
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Edfeldt NBF, Harwood EA, Sigurdsson ST, Hopkins PB, Reid BR. Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links. Nucleic Acids Res 2004; 32:2795-801. [PMID: 15155848 PMCID: PMC419608 DOI: 10.1093/nar/gkh607] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the preceding paper in this journal, we described the solution structure of the nitrous acid cross-linked dodecamer duplex [d(GCATCCGGATGC)]2 (the cross-linked guanines are underlined). The structure revealed that the cross-linked guanines form a nearly planar covalently linked 'G:G base pair', with the complementary partner cytidines flipped out of the helix. Here we explore the flanking sequence context effect on the structure of nitrous acid cross-links in [d(CG)]2 and the factors allowing the extrahelical cytidines to adopt such fixed positions in the minor groove. We have used NMR spectroscopy to determine the solution structure of a second cross-linked dodecamer duplex, [d(CGCTACGTAGCG)]2, which shows that the identity of the flanking base pairs significantly alters the stacking patterns and phosphate backbone conformations. The cross-linked guanines are now stacked well on adenines preceding the extrahelical cytidines, illustrating the importance of purine- purine base stacking. Observation of an imino proton resonance at 15.6 p.p.m. provides evidence for hydrogen bonding between the two cross-linked guanines. Preliminary structural studies on the cross-linked duplex [d(CGCGACGTCGCG)]2 show that the extrahelical cytidines are very mobile in this sequence context. We suggest that favorable van der Waals interactions between the cytidine and the adenine 2 bp away from the cross-link localize the cytidines in the previous cross-linked structures.
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Teplukhin AV, Malenkov GG, Poltev VI. Monte Carlo simulation of DNA fragment hydration in the presence of alkaline cations using novel atom-atom potential functions. J Biomol Struct Dyn 1998; 16:289-300. [PMID: 9833668 DOI: 10.1080/07391102.1998.10508247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The set of atom-atom potential functions specially adjusted to simulation of nucleic acid fragment hydration (Poltev, Grokhlina & Malenkov, J. Biomol. Struct. Dyn. 2, 413, 1984) is extended by including alkaline cation interactions. The choice of new potential functions was realized using experimental data on crystal hydrates of nucleotides and related compounds as well as thermodynamic data on ion solutions. The extended set of potential functions allows to reproduce many features of interactions between alkaline cations and nucleic acid fragments in water solutions. The sites of preferential cation localization near bases and phosphate groups were obtained and examined. The potential functions reproduce the dissociation tendency of cation-phosphate group and cation-base complexes in aqueous medium. Pathways of cation dissociations from nucleic acid components have been studied, and metastable water-bridged positions of cations near bases and phosphate group have been revealed.
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Affiliation(s)
- A V Teplukhin
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow region
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Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL. The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method. J Biomol Struct Dyn 1997; 15:69-80. [PMID: 9283981 DOI: 10.1080/07391102.1997.10508947] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An extensive computer simulation of nucleic acid bases and Watson-Crick base pairs in a water cluster and DMSO cluster is performed by the Monte Carlo method. It is demonstrated that the unfavorable energetics of pair formation in a water cluster is determined by the significant destabilizing contribution of solvent to the energy of complex formation. It is shown that the formation of coplanar base pairs in a DMSO cluster is favorable. The DMSO cluster stabilizes A-U and A-T base pairs and the insignificant destabilization of the G-C base pair by a DMSO cluster is much less than the stabilization which occurs due to the attraction between bases.
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Affiliation(s)
- V I Danilov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
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