1
|
Liu S, Yang Q, Zhang L, Luo S. Accurate Protein p Ka Prediction with Physical Organic Chemistry Guided 3D Protein Representation. J Chem Inf Model 2024; 64:4410-4418. [PMID: 38780156 DOI: 10.1021/acs.jcim.4c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Protein pKa is a fundamental physicochemical parameter that dictates protein structure and function. However, accurately determining protein site-pKa values remains a substantial challenge, both experimentally and theoretically. In this study, we introduce a physical organic approach, leveraging a protein structural and physical-organic-parameter-based representation (P-SPOC), to develop a rapid and intuitive model for protein pKa prediction. Our P-SPOC model achieves state-of-the-art predictive accuracy, with a mean absolute error (MAE) of 0.33 pKa units. Furthermore, we have incorporated advanced protein structure prediction models, like AlphaFold2, to approximate structures for proteins lacking three-dimensional representations, which enhances the applicability of our model in the context of structure-undetermined protein research. To promote broader accessibility within the research community, an online prediction interface was also established at isyn.luoszgroup.com.
Collapse
Affiliation(s)
- Siyuan Liu
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qi Yang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Long Zhang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Sanzhong Luo
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
2
|
Mehta MJ, Kim HJ, Lim SB, Naito M, Miyata K. Recent Progress in the Endosomal Escape Mechanism and Chemical Structures of Polycations for Nucleic Acid Delivery. Macromol Biosci 2024; 24:e2300366. [PMID: 38226723 DOI: 10.1002/mabi.202300366] [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: 08/10/2023] [Revised: 12/22/2023] [Indexed: 01/17/2024]
Abstract
Nucleic acid-based therapies are seeing a spiralling surge. Stimuli-responsive polymers, especially pH-responsive ones, are gaining widespread attention because of their ability to efficiently deliver nucleic acids. These polymers can be synthesized and modified according to target requirements, such as delivery sites and the nature of nucleic acids. In this regard, the endosomal escape mechanism of polymer-nucleic acid complexes (polyplexes) remains a topic of considerable interest owing to various plausible escape mechanisms. This review describes current progress in the endosomal escape mechanism of polyplexes and state-of-the-art chemical designs for pH-responsive polymers. The importance is also discussed of the acid dissociation constant (i.e., pKa) in designing the new generation of pH-responsive polymers, along with assays to monitor and quantify the endosomal escape behavior. Further, the use of machine learning is addressed in pKa prediction and polymer design to find novel chemical structures for pH responsiveness. This review will facilitate the design of new pH-responsive polymers for advanced and efficient nucleic acid delivery.
Collapse
Affiliation(s)
- Mohit J Mehta
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
- Department of Biological Engineering, College of Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Sung Been Lim
- Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon, 22212, Republic of Korea
| | - Mitsuru Naito
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| |
Collapse
|
3
|
Sanchez AJ, Maier S, Raghavachari K. Leveraging DFT and Molecular Fragmentation for Chemically Accurate p Ka Prediction Using Machine Learning. J Chem Inf Model 2024; 64:712-723. [PMID: 38301279 DOI: 10.1021/acs.jcim.3c01923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
We present a quantum mechanical/machine learning (ML) framework based on random forest to accurately predict the pKas of complex organic molecules using inexpensive density functional theory (DFT) calculations. By including physics-based features from low-level DFT calculations and structural features from our connectivity-based hierarchy (CBH) fragmentation protocol, we can correct the systematic error associated with DFT. The generalizability and performance of our model are evaluated on two benchmark sets (SAMPL6 and Novartis). We believe the carefully curated input of physics-based features lessens the model's data dependence and need for complex deep learning architectures, without compromising the accuracy of the test sets. As a point of novelty, our work extends the applicability of CBH, employing it for the generation of viable molecular descriptors for ML.
Collapse
Affiliation(s)
- Alec J Sanchez
- Department of Chemistry, Indiana University?, Bloomington, Indiana 47405, United States
| | - Sarah Maier
- Department of Chemistry, Indiana University?, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University?, Bloomington, Indiana 47405, United States
| |
Collapse
|
4
|
Hurley MFD, Raddi RM, Pattis JG, Voelz VA. Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge. Phys Chem Chem Phys 2023; 25:32393-32406. [PMID: 38009066 PMCID: PMC10760931 DOI: 10.1039/d3cp02197a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
As part of the SAMPL9 community-wide blind host-guest challenge, we implemented an expanded ensemble workflow to predict absolute binding free energies for 13 small molecules against pillar[6]arene. Notable features of our protocol include consideration of a variety of protonation and enantiomeric states for both host and guests, optimization of alchemical intermediates, and analysis of free energy estimates and their uncertainty using large numbers of simulation replicates performed using distributed computing. Our predictions of absolute binding free energies resulted in a mean absolute error of 2.29 kcal mol-1 and an R2 of 0.54. Overall, results show that expanded ensemble calculations using all-atom molecular dynamics simulations are a valuable and efficient computational tool in predicting absolute binding free energies.
Collapse
Affiliation(s)
| | - Robert M Raddi
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
| | - Jason G Pattis
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
| |
Collapse
|
5
|
Alcázar JJ, Misad Saide AC, Campodónico PR. Reliable and accurate prediction of basic pK[Formula: see text] values in nitrogen compounds: the pK[Formula: see text] shift in supramolecular systems as a case study. J Cheminform 2023; 15:90. [PMID: 37770903 PMCID: PMC10540475 DOI: 10.1186/s13321-023-00763-3] [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: 06/29/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
This article presents a quantitative structure-activity relationship (QSAR) approach for predicting the acid dissociation constant (pK[Formula: see text]) of nitrogenous compounds, including those within supramolecular complexes based on cucurbiturils. The model combines low-cost quantum mechanical calculations with QSAR methodology and linear regressions to achieve accurate predictions for a broad range of nitrogen-containing compounds. The model was developed using a diverse dataset of 130 nitrogenous compounds and exhibits excellent predictive performance, with a high coefficient of determination (R[Formula: see text]) of 0.9905, low standard error (s) of 0.3066, and high Fisher statistic (F) of 2142. The model outperforms existing methods, such as Chemaxon software and previous studies, in terms of accuracy and its ability to handle heterogeneous datasets. External validation on pharmaceutical ingredients, dyes, and supramolecular complexes based on cucurbiturils confirms the reliability of the model. To enhance usability, a script-like tool has been developed, providing a streamlined process for users to access the model. This study represents a significant advancement in pK[Formula: see text] prediction, offering valuable insights for drug design and supramolecular system optimization.
Collapse
Affiliation(s)
- Jackson J. Alcázar
- Centro de Química Médica, Universidad del Desarrollo, Av.Plaza 680, 7780272 Santiago, RM Chile
| | | | - Paola R. Campodónico
- Centro de Química Médica, Universidad del Desarrollo, Av.Plaza 680, 7780272 Santiago, RM Chile
| |
Collapse
|
6
|
Wang B, Zhang Z, Dong Y, Qiu Y, Ren J, Bi K, Ji X, Liu C, Zhou L, Dai Y. Machine-Learning-Enabled Ligand Screening for Cs/Sr Crystallizing Separation. Inorg Chem 2023; 62:13293-13303. [PMID: 37557894 DOI: 10.1021/acs.inorgchem.3c01564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The reprocessing of spent nuclear fuel is critical for the sustainability of the nuclear energy industry. However, several key separation processes present challenges in this regard, calling for continuous research into next-generation separation materials. Herein, we propose a high-throughput screening framework to improve efficiency in identifying potential ligands that selectively coordinate metal cations of interest in liquid wastes that considers multiple key chemical characteristics, including aqueous solubility, pKa, and coordination bond length. Machine-learning models were designed for the fast and accurate prediction of these characteristics by using graph convolution and transfer-learning techniques. Suitable ligands for Cs/Sr crystallizing separation were identified through the "computational funnel", and several top-ranking, nontoxic, low-cost ligands were selected for experimental verification.
Collapse
Affiliation(s)
- Bingbing Wang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Zhiyuan Zhang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yue Dong
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yuqing Qiu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Junyu Ren
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Kexin Bi
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Xu Ji
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Chong Liu
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Li Zhou
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yiyang Dai
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| |
Collapse
|
7
|
Lv J, Wang XY, Chang S, Xi CY, Wu X, Chen BB, Guo ZQ, Li DW, Qian RC. Amperometric Identification of Single Exosomes and Their Dopamine Contents Secreted by Living Cells. Anal Chem 2023. [PMID: 37478050 DOI: 10.1021/acs.analchem.3c01253] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Dopamine (DA) is an important neurotransmitter, which not only participates in the regulation of neural processes but also plays critical roles in tumor progression and immunity. However, direct identification of DA-containing exosomes, as well as quantification of DA in single vesicles, is still challenging. Here, we report a nanopipette-assisted method to detect single exosomes and their dopamine contents via amperometric measurement. The resistive-pulse current measured can simultaneously provide accurate information of vesicle translocation and DA contents in single exosomes. Accordingly, DA-containing exosomes secreted from HeLa and PC12 cells under different treatment modes successfully detected the DA encapsulation efficiency and the amount of exosome secretion that distinguish between cell types. Furthermore, a custom machine learning model was constructed to classify the exosome signals from different sources, with an accuracy of more than 99%. Our strategy offers a useful tool for investigating single exosomes and their DA contents, which facilitates the analysis of DA-containing exosomes derived from other untreated or stimulated cells and may open up a new insight to the research of DA biology.
Collapse
Affiliation(s)
- Jian Lv
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiao-Yuan Wang
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Shuai Chang
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Cheng-Ye Xi
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xue Wu
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Bin-Bin Chen
- Shenzhen Institute of Aggregate Science and Technology, School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, P. R. China
| | - Zhi-Qian Guo
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Da-Wei Li
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Ruo-Can Qian
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Joint International Laboratory for Precision Chemistry, Frontiers Science Center for Materiobiology & Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| |
Collapse
|
8
|
Yan Y, Wang Q, Hao P, Zhou H, Kong X, Li Z, Shao M. Photoassisted Strategy to Promote Glycerol Electrooxidation to Lactic Acid Coupled with Hydrogen Production. ACS APPLIED MATERIALS & INTERFACES 2023; 15:23265-23275. [PMID: 37146267 DOI: 10.1021/acsami.3c02591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Electrocatalytic oxidation of glycerol (GLY; from a biodiesel byproduct) to lactic acid (LA; the key monomers for polylactic acid; PLA) is considered a sustainable approach for biomass waste upcycling and is coupled with cathodic hydrogen (H2) production. However, current research still suffer from issues of low current density and low LA selectivity. Herein, we reported a photoassisted electrocatalytic strategy to achieve the selective oxidation of GLY to LA over a gold nanowire (Au NW) catalyst, attaining a high current density of 387 mA cm-2 at 0.95 V vs RHE, together with a high LA selectivity of 80%, outperforming most of the reported works in the literature. We reveal that the light-assistance strategy plays a dual role, which can both accelerate the reaction rate through the photothermal effect and also promote the adsorption of the middle hydroxyl of GLY over Au NWs to realize the selective oxidation of GLY to LA. As a proof-of-concept, we realized the direct conversion of crude GLY that was extracted from cooking oil to attain LA and coupled it with H2 production using the developed photoassisted electrooxidation process, revealing the potential of this strategy in practical applications.
Collapse
Affiliation(s)
- Yifan Yan
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qiangyu Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Pengjie Hao
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hua Zhou
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
- Quzhou Institute for Innovation in Resource Chemical Engineering, Quzhou 324000, China
| | - Xianggui Kong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
- Quzhou Institute for Innovation in Resource Chemical Engineering, Quzhou 324000, China
| | - Zhenhua Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
- Quzhou Institute for Innovation in Resource Chemical Engineering, Quzhou 324000, China
| | - Mingfei Shao
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
- Quzhou Institute for Innovation in Resource Chemical Engineering, Quzhou 324000, China
| |
Collapse
|
9
|
Thermodynamic and Kinetic Studies of the Activities of Aldehydic C−H Bonds toward Their H‐Atom Transfer Reactions. ChemistrySelect 2023. [DOI: 10.1002/slct.202204789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
|
10
|
Jiao X, Huang W, Wang A, Wu B, Kang Q, Luo X, Bai L, Deng Z. Crystallographic Deciphering of Spontaneous Self-Assembly of Achiral Calciphores to Chiral Complexes. Chemistry 2023; 29:e202203127. [PMID: 36408990 DOI: 10.1002/chem.202203127] [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: 10/07/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Thiapyricins (TPC-A/B, 1 and 2), which are new metallophore scaffolds exhibiting selective divalent cation binding property, were produced in response to metal-deprived conditions by Saccharothrix sp. TRM_47004 isolated from the Lop Nor Salt Lake. TPCs represent a thiazolyl-pyridine skeleton of a calcium-binding natural product, calciphore, owing to the selectivity to calcium ions among diverse metal ions. The thiapyricins exhibited notable co-crystalline characteristics of the apo- and holo-forms with racemic enantiomers comprising a pair of space isomers in a Δ/Λ-form. Therefore, we postulated a mechanism for the four-hierarchical self-assembly of achiral natural products into chiral complexes. Furthermore, their metal-chelating trait aided the adaptation of the host during metal starvation by increasing the production of TPCs. This study presents a structural paradigm of a new calciphore, provides insight into the mechanism of natural product assembly, and highlights the causality between the production of the metallophore and metallic habitats.
Collapse
Affiliation(s)
- Xingzhi Jiao
- State Key Laboratory of, Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Wei Huang
- College of Life Science, Tarim University, 843300, Alar, Xinjiang, P. R. China
| | - Anqi Wang
- State Key Laboratory of, Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Banghao Wu
- State Key Laboratory of, Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Qianjin Kang
- State Key Laboratory of, Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Xiaoxia Luo
- College of Life Science, Tarim University, 843300, Alar, Xinjiang, P. R. China
| | - Linquan Bai
- State Key Laboratory of, Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.,College of Life Science, Tarim University, 843300, Alar, Xinjiang, P. R. China
| | - Zixin Deng
- State Key Laboratory of, Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research, Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| |
Collapse
|
11
|
Light-induced phosphine-catalyzed asymmetric functionalization of benzylic C-H bonds. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1406-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
12
|
Qian B, Zhang L, Zhang G, Fu Y, Zhu X, Shen G. Thermodynamic Evaluation on Alkoxyamines of TEMPO Derivatives, Stable Alkoxyamines or Potential Radical Donors? ChemistrySelect 2022. [DOI: 10.1002/slct.202204144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Bao‐Chen Qian
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| | - Lu Zhang
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| | - Gao‐Shuai Zhang
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| | - Yan‐Hua Fu
- College of Chemistry and Environmental Engineering Anyang Institute of Technology Anyang Henan 455000 P. R. China
| | - Xiao‐Qing Zhu
- The State Key Laboratory of Elemento-Organic Chemistry Department of Chemistry Nankai University Tianjin 300071 P. R. China
| | - Guang‐Bin Shen
- School of Medical Engineering Jining Medical University Jining Shandong 272000 P. R. China
| |
Collapse
|
13
|
Wu M, Wu G, Lu F, Wang H, Lei A, Wang J. Microalgal photoautotrophic growth induces pH decrease in the aquatic environment by acidic metabolites secretion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:115. [PMID: 36289523 PMCID: PMC9608927 DOI: 10.1186/s13068-022-02212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/08/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Microalgae can absorb CO2 during photosynthesis, which causes the aquatic environmental pH to rise. However, the pH is reduced when microalga Euglena gracilis (EG) is cultivated under photoautotrophic conditions. The mechanism behind this unique phenomenon is not yet elucidated. RESULTS The present study evaluated the growth of EG, compared to Chlorella vulgaris (CV), as the control group; analyzed the dissolved organic matter (DOM) in the aquatic environment; finally revealed the mechanism of the decrease in the aquatic environmental pH via comparative metabolomics analysis. Although the CV cell density was 28.3-fold that of EG, the secreted-DOM content from EG cell was 49.8-fold that of CV (p-value < 0.001). The main component of EG's DOM was rich in humic acids, which contained more DOM composed of chemical bonds such as N-H, O-H, C-H, C=O, C-O-C, and C-OH than that of CV. Essentially, the 24 candidate biomarkers metabolites secreted by EG into the aquatic environment were acidic substances, mainly lipids and lipid-like molecules, organoheterocyclic compounds, organic acids, and derivatives. Moreover, six potential critical secreted-metabolic pathways were identified. CONCLUSIONS This study demonstrated that EG secreted acidic metabolites, resulting in decreased aquatic environmental pH. This study provides novel insights into a new understanding of the ecological niche of EG and the rule of pH change in the microalgae aquatic environment.
Collapse
Affiliation(s)
- Mingcan Wu
- grid.263488.30000 0001 0472 9649Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China ,grid.428986.90000 0001 0373 6302State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, 570228 China
| | - Guimei Wu
- grid.428986.90000 0001 0373 6302State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, 570228 China
| | - Feimiao Lu
- grid.428986.90000 0001 0373 6302State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou, 570228 China
| | - Hongxia Wang
- grid.9227.e0000000119573309Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 China
| | - Anping Lei
- grid.263488.30000 0001 0472 9649Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| | - Jiangxin Wang
- grid.263488.30000 0001 0472 9649Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 China
| |
Collapse
|
14
|
Shi M, Zhang Q, Gao J, Mi X, Luo S. Catalytic Asymmetric α‐Alkylsulfenylation with a Disulfide Reagent. Angew Chem Int Ed Engl 2022; 61:e202209044. [DOI: 10.1002/anie.202209044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Mingying Shi
- College of Chemistry Beijing Normal University Beijing 100875 China
| | - Qi Zhang
- Center of Basic Molecular Science (CBMS) Department of Chemistry Tsinghua University Beijing 100084 China
| | - Jiali Gao
- College of Chemistry Beijing Normal University Beijing 100875 China
| | - Xueling Mi
- College of Chemistry Beijing Normal University Beijing 100875 China
| | - Sanzhong Luo
- Center of Basic Molecular Science (CBMS) Department of Chemistry Tsinghua University Beijing 100084 China
| |
Collapse
|
15
|
Shi M, Zhang Q, Gao J, Mi X, Luo S. Catalytic Asymmetric α‐Alkylsulfenylation with a Disulfide Reagent. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mingying Shi
- Beijing Normal University Department of Chemistry CHINA
| | - Qi Zhang
- Tsinghua University CBMS, Department of Chemistry CHINA
| | - Jiali Gao
- Beijing Normal University Department of Chemistry CHINA
| | - Xueling Mi
- Beijing Normal University Department of Chemistry CHINA
| | - Sanzhong Luo
- Tsinghua University Department of Chemistry Tsinghua University 100084 Beijing CHINA
| |
Collapse
|
16
|
Li E, Chen J, Huang Y. Enantioselective Seleno‐Michael Addition Reactions Catalyzed by a Chiral Bifunctional N‐Heterocyclic Carbene with Noncovalent Activation. Angew Chem Int Ed Engl 2022; 61:e202202040. [DOI: 10.1002/anie.202202040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 11/08/2022]
Affiliation(s)
- En Li
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Shenzhen 518055 China
- Pingshan Translational Medicine Center Shenzhen Bay Laboratory Shenzhen 518118 China
| | - Jiean Chen
- Pingshan Translational Medicine Center Shenzhen Bay Laboratory Shenzhen 518118 China
| | - Yong Huang
- Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong SAR China
| |
Collapse
|
17
|
Yang Q, Liu Y, Cheng J, Li Y, Liu S, Duan Y, Zhang L, Luo S. An Ensemble Structure and Physiochemical (SPOC) Descriptor for Machine-Learning Prediction of Chemical Reaction and Molecular Properties. Chemphyschem 2022; 23:e202200255. [PMID: 35478429 DOI: 10.1002/cphc.202200255] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 11/08/2022]
Abstract
Feature representations, or descriptors, are machines' chemical language that largely shapes the prediction capability, generalizability and interpretability of machine learning models. To develop a generally applicable descriptor is highly warranted for chemists to deal with conventional prediction tasks in the context of sparsely distributed and small datasets. Inspired by the chemist's vision on molecules, we presented herein an ensemble descriptor, SPOC, curated on the principles of physical organic chemistry that integrates Structure and Physicochemical property (SPOC) of a molecule. SPOC could be readily constructed by combining molecular fingerprints, representing the structure of a given molecule, and molecular physicochemical properties extracted from RDKit or Mordred molecular descriptors. The applicability of SPOC was fully surveyed in a range of well-structured chemical databases with machine learning tasks varying from regression to classifications.
Collapse
Affiliation(s)
- Qi Yang
- Tsinghua University, CBMS, Department of Chemistry, CHINA
| | - Yidi Liu
- Tsinghua University, CBMS, Department of Chemistry, CHINA
| | - Junjie Cheng
- Tsinghua University, CBMS, Department of Chemistry, CHINA
| | - Yao Li
- Tsinghua University, CBMS, Department of Chemistry, CHINA
| | - Siyuan Liu
- Tsinghua University, CBMS, Department of Chemistry, CHINA
| | - Yingdong Duan
- Tsinghua University, CBMS, Department of Chemistry, CHINA
| | - Long Zhang
- Tsinghua University, CBMS, Department of Chemistry, CHINA
| | - Sanzhong Luo
- Tsinghua University, Department of Chemistry, Tsinghua University, 100084, Beijing, CHINA
| |
Collapse
|
18
|
Li E, Chen J, Huang Y. Enantioselective Seleno‐Michael Addition Reactions Catalyzed by a Chiral Bifunctional N‐Heterocyclic Carbene with Noncovalent Activation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- En Li
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Shenzhen 518055 China
- Pingshan Translational Medicine Center Shenzhen Bay Laboratory Shenzhen 518118 China
| | - Jiean Chen
- Pingshan Translational Medicine Center Shenzhen Bay Laboratory Shenzhen 518118 China
| | - Yong Huang
- Department of Chemistry The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong SAR China
| |
Collapse
|
19
|
Aliagas I, Gobbi A, Lee ML, Sellers BD. Comparison of logP and logD correction models trained with public and proprietary data sets. J Comput Aided Mol Des 2022; 36:253-262. [PMID: 35359246 DOI: 10.1007/s10822-022-00450-9] [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: 10/05/2021] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
Abstract
In drug discovery, partition and distribution coefficients, logP and logD for octanol/water, are widely used as metrics of the lipophilicity of molecules, which in turn have a strong influence on the bioactivity and bioavailability of potential drugs. There are a variety of established methods, mostly fragment or atom-based, to calculate logP while logD prediction generally relies on calculated logP and pKa for the estimation of neutral and ionized populations at a given pH. Algorithms such as ClogP have limitations generally leading to systematic errors for chemically related molecules while pKa estimation is generally more difficult due to the interplay of electronic, inductive and conjugation effects for ionizable moieties. We propose an integrated machine learning QSAR modeling approach to predict logD by training the model with experimental data while using ClogP and pKa predicted by commercial software as model descriptors. By optimizing the loss function for the ClogD calculated by the software, we build a correction model that incorporates both descriptors from the software and available experimental logD data. Additionally, we calculate logP from the logD model using the software predicted pKa's. Here, we have trained models using publicly or commercial available logD data to show that this approach can improve on commercial software predictions of lipophilicity. When applied to other logD data sets, this approach extends the domain of applicability of logD and logP predictions over commercial software. Performance of these models favorably compare with models built with a larger set of proprietary logD data.
Collapse
Affiliation(s)
- Ignacio Aliagas
- Discovery Chemistry, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Man-Ling Lee
- Discovery Chemistry, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Benjamin D Sellers
- Discovery Chemistry, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| |
Collapse
|
20
|
Zheng W, Ma Z, Sun W, Zhao L. Target High‐efficiency Ionic Liquids to Promote
H
2
SO
4
‐catalyzed
C4
Alkylation by Machine Learning. AIChE J 2022. [DOI: 10.1002/aic.17698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Weizhong Zheng
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering East China University of Science and Technology Shanghai China
| | - Zhihong Ma
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering East China University of Science and Technology Shanghai China
| | - Weizhen Sun
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering East China University of Science and Technology Shanghai China
| | - Ling Zhao
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering East China University of Science and Technology Shanghai China
| |
Collapse
|
21
|
Kang QK, Li Y, Chen K, Zhu H, Wu WQ, Lin Y, Shi H. Rhodium-Catalyzed Stereoselective Deuteration of Benzylic C-H Bonds via Reversible η 6 -Coordination. Angew Chem Int Ed Engl 2022; 61:e202117381. [PMID: 35006640 DOI: 10.1002/anie.202117381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Indexed: 12/15/2022]
Abstract
We report a convenient method for benzylic H/D exchange of a wide variety of substrates bearing primary, secondary, or tertiary C-H bonds via a reversible η6 -coordination strategy. A doubly cationic [CpCF3 RhIII ]2+ catalyst that serves as an arenophile facilitates deprotonation of inert benzylic hydrogen atoms (pKa >40 in DMSO) without affecting other hydrogen atoms, such as those on aromatic rings or in α-positions of carboxylate groups. Notably, the H/D exchange reactions feature high stereoretention. We demonstrated the potential utility of this method by using it for deuterium labeling of ten pharmaceuticals and their analogues.
Collapse
Affiliation(s)
- Qi-Kai Kang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Yuntong Li
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Kai Chen
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Hui Zhu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Wen-Qiang Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Yunzhi Lin
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Hang Shi
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| |
Collapse
|
22
|
Kang QK, Li Y, Chen K, Zhu H, Wu WQ, Lin Y, Shi H. Rhodium‐Catalyzed Stereoselective Deuteration of Benzylic C–H Bonds via Reversible η6‐Coordination. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qi-Kai Kang
- Westlake University School of Science 18,Shilongshan RoadCloud Town, Xihu District 310024 Hangzhou CHINA
| | - Yuntong Li
- Westlake University School of Science 18,Shilongshan RoadCloud Town, Xihu District 310024 Hangzhou CHINA
| | - Kai Chen
- Westlake University School of Science 18,Shilongshan RoadCloud Town, Xihu District 310024 Hangzhou CHINA
| | - Hui Zhu
- Westlake University School of Science 18,Shilongshan RoadCloud Town, Xihu District 310024 Hangzhou CHINA
| | - Wen-Qiang Wu
- Westlake University School of Science 18,Shilongshan RoadCloud Town, Xihu District 310024 Hangzhou CHINA
| | - Yunzhi Lin
- Westlake University School of Science 18,Shilongshan RoadCloud Town, Xihu District 310024 Hangzhou CHINA
| | - Hang Shi
- Westlake University School of Science 18 Shilongshan Road 310024 Hangzhou CHINA
| |
Collapse
|
23
|
Network Biology and Artificial Intelligence Drive the Understanding of the Multidrug Resistance Phenotype in Cancer. Drug Resist Updat 2022; 60:100811. [DOI: 10.1016/j.drup.2022.100811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/07/2023]
|
24
|
Raman G. Study of the Relationship between Synthesis Descriptors and the Type of Zeolite Phase Formed in ZSM‐43 Synthesis by Using Machine Learning. ChemistrySelect 2021. [DOI: 10.1002/slct.202102890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ganesan Raman
- Reliance Research & Development Center Reliance Corporate Park, Reliance Industries Limited Thane-Belapur Road, Ghansoli Navi Mumbai India 400701
| |
Collapse
|
25
|
Racioppi S, Rahm M. In-Situ Electronegativity and the Bridging of Chemical Bonding Concepts. Chemistry 2021; 27:18156-18167. [PMID: 34668618 PMCID: PMC9299076 DOI: 10.1002/chem.202103477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/30/2022]
Abstract
One challenge in chemistry is the plethora of often disparate models for rationalizing the electronic structure of molecules. Chemical concepts abound, but their connections are often frail. This work describes a quantum‐mechanical framework that enables a combination of ideas from three approaches common for the analysis of chemical bonds: energy decomposition analysis (EDA), quantum chemical topology, and molecular orbital (MO) theory. The glue to our theory is the electron energy density, interpretable as one part electrons and one part electronegativity. We present a three‐dimensional analysis of the electron energy density and use it to redefine what constitutes an atom in a molecule. Definitions of atomic partial charge and electronegativity follow in a way that connects these concepts to the total energy of a molecule. The formation of polar bonds is predicted to cause inversion of electronegativity, and a new perspective of bonding in diborane and guanine−cytosine base‐pairing is presented. The electronegativity of atoms inside molecules is shown to be predictive of pKa.
Collapse
Affiliation(s)
- Stefano Racioppi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemigården 4, 41258, Gothenburg, Sweden
| | - Martin Rahm
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemigården 4, 41258, Gothenburg, Sweden
| |
Collapse
|
26
|
Raddi RM, Voelz VA. Stacking Gaussian processes to improve [Formula: see text] predictions in the SAMPL7 challenge. J Comput Aided Mol Des 2021; 35:953-961. [PMID: 34363562 PMCID: PMC9478567 DOI: 10.1007/s10822-021-00411-8] [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: 04/12/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Accurate predictions of acid dissociation constants are essential to rational molecular design in the pharmaceutical industry and elsewhere. There has been much interest in developing new machine learning methods that can produce fast and accurate pKa predictions for arbitrary species, as well as estimates of prediction uncertainty. Previously, as part of the SAMPL6 community-wide blind challenge, Bannan et al. approached the problem of predicting [Formula: see text]s by using a Gaussian process regression to predict microscopic [Formula: see text]s, from which macroscopic [Formula: see text] values can be analytically computed (Bannan et al. in J Comput-Aided Mol Des 32:1165-1177). While this method can make reasonably quick and accurate predictions using a small training set, accuracy was limited by the lack of a sufficiently broad range of chemical space in the training set (e.g., the inclusion of polyprotic acids). Here, to address this issue, we construct a deep Gaussian Process (GP) model that can include more features without invoking the curse of dimensionality. We trained both a standard GP and a deep GP model using a database of approximately 3500 small molecules curated from public sources, filtered by similarity to targets. We tested the model on both the SAMPL6 and more recent SAMPL7 challenge, which introduced a similar lack of ionizable sites and/or environments found between the test set and the previous training set. The results show that while the deep GP model made only minor improvements over the standard GP model for SAMPL6 predictions, it made significant improvements over the standard GP model in SAMPL7 macroscopic predictions, achieving a MAE of 1.5 [Formula: see text].
Collapse
Affiliation(s)
- Robert M Raddi
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| |
Collapse
|
27
|
Pan X, Wang H, Li C, Zhang JZH, Ji C. MolGpka: A Web Server for Small Molecule p Ka Prediction Using a Graph-Convolutional Neural Network. J Chem Inf Model 2021; 61:3159-3165. [PMID: 34251213 DOI: 10.1021/acs.jcim.1c00075] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
pKa is an important property in the lead optimization process since the charge state of a molecule in physiologic pH plays a critical role in its biological activity, solubility, membrane permeability, metabolism, and toxicity. Accurate and fast estimation of small molecule pKa is vital during the drug discovery process. We present MolGpKa, a web server for pKa prediction using a graph-convolutional neural network model. The model works by learning pKa related chemical patterns automatically and building reliable predictors with learned features. ACD/pKa data for 1.6 million compounds from the ChEMBL database was used for model training. We found that the performance of the model is better than machine learning models built with human-engineered fingerprints. Detailed analysis shows that the substitution effect on pKa is well learned by the model. MolGpKa is a handy tool for the rapid estimation of pKa during the ligand design process. The MolGpKa server is freely available to researchers and can be accessed at https://xundrug.cn/molgpka.
Collapse
Affiliation(s)
- Xiaolin Pan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Hao Wang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Cuiyu Li
- Advanced Computing East China Sub-center, Suma Technology Co., Ltd., Kunshan 215300, China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| |
Collapse
|