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Lu J, Liang W, Hu Y, Zhang X, Yu P, Cai M, Xie D, Zhou Q, Zhou X, Liu Y, Wang J, Guo J, Tang L. Metabolism characterization and toxicity of N-hydap, a marine candidate drug for lung cancer therapy by LC-MS method. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:33. [PMID: 38771401 PMCID: PMC11109052 DOI: 10.1007/s13659-024-00455-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024]
Abstract
N-Hydroxyapiosporamide (N-hydap), a marine product derived from a sponge-associated fungus, has shown promising inhibitory effects on small cell lung cancer (SCLC). However, there is limited understanding of its metabolic pathways and characteristics. This study explored the in vitro metabolic profiles of N-hydap in human recombinant cytochrome P450s (CYPs) and UDP-glucuronosyltransferases (UGTs), as well as human/rat/mice microsomes, and also the pharmacokinetic properties by HPLC-MS/MS. Additionally, the cocktail probe method was used to investigate the potential to create drug-drug interactions (DDIs). N-Hydap was metabolically unstable in various microsomes after 1 h, with about 50% and 70% of it being eliminated by CYPs and UGTs, respectively. UGT1A3 was the main enzyme involved in glucuronidation (over 80%), making glucuronide the primary metabolite. Despite low bioavailability (0.024%), N-hydap exhibited a higher distribution in the lungs (26.26%), accounting for its efficacy against SCLC. Administering N-hydap to mice at normal doses via gavage did not result in significant toxicity. Furthermore, N-hydap was found to affect the catalytic activity of drug metabolic enzymes (DMEs), particularly increasing the activity of UGT1A3, suggesting potential for DDIs. Understanding the metabolic pathways and properties of N-hydap should improve our knowledge of its drug efficacy, toxicity, and potential for DDIs.
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Affiliation(s)
- Jindi Lu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Weimin Liang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yiwei Hu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xi Zhang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ping Yu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Meiqun Cai
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Danni Xie
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qiong Zhou
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Junfeng Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Jiayin Guo
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Lan Tang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, Southern Medical University Hospital of Integrated Traditional Chinese and Western Medicine, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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2
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Gu Y, Yu Z, Wang Y, Chen L, Lou C, Yang C, Li W, Liu G, Tang Y. admetSAR3.0: a comprehensive platform for exploration, prediction and optimization of chemical ADMET properties. Nucleic Acids Res 2024:gkae298. [PMID: 38647076 DOI: 10.1093/nar/gkae298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Absorption, distribution, metabolism, excretion and toxicity (ADMET) properties play a crucial role in drug discovery and chemical safety assessment. Built on the achievements of admetSAR and its successor, admetSAR2.0, this paper introduced the new version of the series, admetSAR3.0, as a comprehensive platform for chemical ADMET assessment, including search, prediction and optimization modules. In the search module, admetSAR3.0 hosted over 370 000 high-quality experimental ADMET data for 104 652 unique compounds, and supplemented chemical structure similarity search function to facilitate read-across. In the prediction module, we introduced comprehensive ADMET endpoints and two new sections for environmental and cosmetic risk assessments, empowering admetSAR3.0 to provide prediction for 119 endpoints, more than double numbers compared to the previous version. Furthermore, the advanced multi-task graph neural network framework offered robust and reliable support for ADMET prediction. In particular, a module named ADMETopt was added to automatically optimize the ADMET properties of query molecules through transformation rules or scaffold hopping. Finally, admetSAR3.0 provides user-friendly interfaces for multiple types of input data, such as SMILES string, chemical structure and batch molecule file, and supports various output types, including digital, chart displays and file downloads. In summary, admetSAR3.0 is anticipated to be a valuable and powerful tool in drug discovery and chemical safety assessment at http://lmmd.ecust.edu.cn/admetsar3/.
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Affiliation(s)
- Yaxin Gu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yimeng Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Long Chen
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Chaofeng Lou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Chen Yang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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3
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Fu L, Shi S, Yi J, Wang N, He Y, Wu Z, Peng J, Deng Y, Wang W, Wu C, Lyu A, Zeng X, Zhao W, Hou T, Cao D. ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support. Nucleic Acids Res 2024:gkae236. [PMID: 38572755 DOI: 10.1093/nar/gkae236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
ADMETlab 3.0 is the second updated version of the web server that provides a comprehensive and efficient platform for evaluating ADMET-related parameters as well as physicochemical properties and medicinal chemistry characteristics involved in the drug discovery process. This new release addresses the limitations of the previous version and offers broader coverage, improved performance, API functionality, and decision support. For supporting data and endpoints, this version includes 119 features, an increase of 31 compared to the previous version. The updated number of entries is 1.5 times larger than the previous version with over 400 000 entries. ADMETlab 3.0 incorporates a multi-task DMPNN architecture coupled with molecular descriptors, a method that not only guaranteed calculation speed for each endpoint simultaneously, but also achieved a superior performance in terms of accuracy and robustness. In addition, an API has been introduced to meet the growing demand for programmatic access to large amounts of data in ADMETlab 3.0. Moreover, this version includes uncertainty estimates in the prediction results, aiding in the confident selection of candidate compounds for further studies and experiments. ADMETlab 3.0 is publicly for access without the need for registration at: https://admetlab3.scbdd.com.
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Affiliation(s)
- Li Fu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Shaohua Shi
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, 999077, P.R. China
| | - Jiacai Yi
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Ningning Wang
- Xiangya Hospital of Central South University, Changsha, Hunan 410008, P.R. China
| | - Yuanhang He
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Zhenxing Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Jinfu Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Youchao Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Wenxuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
| | - Chengkun Wu
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Aiping Lyu
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, 999077, P.R. China
| | - Xiangxiang Zeng
- Department of Computer Science, Hunan University, Changsha, Hunan 410082, P.R. China
| | - Wentao Zhao
- School of Computer Science, National University of Defense Technology, Changsha, Hunan 410073, P.R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, P.R. China
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4
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Alshehri MM, Kumar N, Kuthi NA, Olaide Z, Alshammari MK, Bello RO, Alghazwni MK, Alshehri AM, Alshlali OM, Ashimiyu-Abdusalam Z, Umar HI. Computer-aided drug discovery of c-Abl kinase inhibitors from plant compounds against chronic myeloid leukemia. J Biomol Struct Dyn 2024:1-21. [PMID: 38517058 DOI: 10.1080/07391102.2024.2329297] [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: 08/21/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
Chronic myeloid leukemia (CML) is a hematological malignancy characterized by the neoplastic transformation of hematopoietic stem cells, driven by the Philadelphia (Ph) chromosome resulting from a translocation between chromosomes 9 and 22. This Ph chromosome harbors the breakpoint cluster region (BCR) and the Abelson (ABL) oncogene (BCR-ABL1) which have a constitutive tyrosine kinase activity. However, the tyrosine kinase activity of BCR-ABL1 have been identified as a key player in CML initiation and maintenance through c-Abl kinase. Despite advancements in tyrosine kinase inhibitors, challenges such as efficacy, safety concerns, and recurring drug resistance persist. This study aims to discover potential c-Abl kinase inhibitors from plant compounds with anti-leukemic properties, employing drug-likeness assessment, molecular docking, in silico pharmacokinetics (ADMET) screening, density function theory (DFT), and molecular dynamics simulations (MDS). Out of 58 screened compounds for drug-likeness, 44 were docked against c-Abl kinase. The top hit compound (isovitexin) and nilotinib (control drug) were subjected to rigorous analyses, including ADMET profiling, DFT evaluation, and MDS for 100 ns. Isovitexin demonstrated a notable binding affinity (-15.492 kcal/mol), closely comparable to nilotinib (-16.826 kcal/mol), showcasing a similar binding pose and superior structural stability and reactivity. While these findings suggest isovitexin as a potential c-Abl kinase inhibitor, further validation through urgent in vitro and in vivo experiments is imperative. This research holds promise for providing an alternative avenue to address existing CML treatment and management challenges.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed M Alshehri
- Pharmaceutical Care Department, Ministry of National Guard-Health Affairs, Riyadh, Kingdom of Saudi Arabia
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles' College of Pharmacy, Udaipur, India
| | - Najwa Ahmad Kuthi
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia (UTM), Johor, Malaysia
| | - Zainab Olaide
- Department of Biochemistry, Ibrahim Badamasi Babangida University, Lapai, Nigeria
| | | | - Ridwan Opeyemi Bello
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
| | | | | | | | - Zainab Ashimiyu-Abdusalam
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research, Yaba, Nigeria
| | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Platform, Federal University of Technology, Akure, Nigeria
- Department of Biochemistry, Federal University of Technology, Akure, Nigeria
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5
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Qi X, Zhao Y, Qi Z, Hou S, Chen J. Machine Learning Empowering Drug Discovery: Applications, Opportunities and Challenges. Molecules 2024; 29:903. [PMID: 38398653 PMCID: PMC10892089 DOI: 10.3390/molecules29040903] [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: 01/15/2024] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Drug discovery plays a critical role in advancing human health by developing new medications and treatments to combat diseases. How to accelerate the pace and reduce the costs of new drug discovery has long been a key concern for the pharmaceutical industry. Fortunately, by leveraging advanced algorithms, computational power and biological big data, artificial intelligence (AI) technology, especially machine learning (ML), holds the promise of making the hunt for new drugs more efficient. Recently, the Transformer-based models that have achieved revolutionary breakthroughs in natural language processing have sparked a new era of their applications in drug discovery. Herein, we introduce the latest applications of ML in drug discovery, highlight the potential of advanced Transformer-based ML models, and discuss the future prospects and challenges in the field.
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Affiliation(s)
- Xin Qi
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215011, China; (Y.Z.); (S.H.); (J.C.)
| | - Yuanchun Zhao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215011, China; (Y.Z.); (S.H.); (J.C.)
| | - Zhuang Qi
- School of Software, Shandong University, Jinan 250101, China;
| | - Siyu Hou
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215011, China; (Y.Z.); (S.H.); (J.C.)
| | - Jiajia Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215011, China; (Y.Z.); (S.H.); (J.C.)
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6
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Abdessadak O, Kandwal P, Alaqarbeh M, Tabti K, Sbai A, Ajana MA, Lakhlifi T, Bouachrine M. Exploring azomethine ylides reactivity with acrolein through cycloaddition reaction and computational antiviral activity assessment against hepatitis C virus. J Mol Model 2024; 30:23. [PMID: 38177613 DOI: 10.1007/s00894-023-05818-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/24/2023] [Indexed: 01/06/2024]
Abstract
CONTEXT The regioselectivity and diastereoselectivity of the 1,3-dipolar cycloaddition reaction between azomethine ylides and acrolein were investigated. The DFT studies revealed that the favored pathway leads to the formation of cis-cycloadduct pyrrolidine and these computational findings align with experimental observations. The cis-cycloadduct pyrrolidine product serves as an advanced intermediate in the synthesis of a hepatitis C virus inhibitor. For this, the antiviral activity of cis-cycloadduct pyrrolidine against cyclophilin A, the co-factor responsible for hepatitis C virus, was also evaluated through molecular docking simulations which revealed intriguing interactions and a high C-score, which were further confirmed by molecular dynamics simulations, demonstrating stability over a 100-ns simulation period. Furthermore, the cis-cycloadduct pyrrolidine exhibits favorable drug-like properties and a better ADMET profile compared to hepatitis C virus inhibitor. METHODS Chemical reactivity studies were performed using DFT method by the functional B3LYP at 6-31G (d, p) computational level by GAUSSIAN 16 program. Frontal molecular orbitals theory used to investigate HOMO/LUMO interactions between azomethine ylides and acrolein. Findings of this approach were confirmed by global reactivity indices and electron displacement was investigated based on Fukui functions. Furthermore, the activation energies were determined after frequency calculations using TS Berny algorithm and transition states were confirmed by the presence of a single imaginary frequency. Moreover, antiviral activity of cis-cycloadduct was explored through molecular docking using Surflex-Dock suite SYBYL X 2.0, and molecular dynamics simulation using GROMACS program. Finally, drug-like properties were investigated with SwissADME and ADMETlab 2.0.
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Affiliation(s)
- Oumayma Abdessadak
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Pankaj Kandwal
- Department of Chemistry, National Institute of Technology, Dehradun, Uttarakhand, 246174, India
| | - Marwa Alaqarbeh
- Basic Science Department, Prince Al Hussein bin Abdullah II Academy for Civil Protection, Al-Balqa Applied University, Al-Salt, 19117, Jordan
| | - Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco.
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory, Faculty of Sciences, Moulay Ismail University, 50000, Meknes, Morocco
- EST Khenifra, Sultan Moulay Sliman University, 23000, Beni-Mellal, Morocco
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7
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Swanson K, Walther P, Leitz J, Mukherjee S, Wu JC, Shivnaraine RV, Zou J. ADMET-AI: A machine learning ADMET platform for evaluation of large-scale chemical libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.28.573531. [PMID: 38234753 PMCID: PMC10793392 DOI: 10.1101/2023.12.28.573531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Summary The emergence of large chemical repositories and combinatorial chemical spaces, coupled with high-throughput docking and generative AI, have greatly expanded the chemical diversity of small molecules for drug discovery. Selecting compounds for experimental validation requires filtering these molecules based on favourable druglike properties, such as Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET). We developed ADMET-AI, a machine learning platform that provides fast and accurate ADMET predictions both as a website and as a Python package. ADMET-AI has the highest average rank on the TDC ADMET Benchmark Group leaderboard, and it is currently the fastest web-based ADMET predictor, with a 45% reduction in time compared to the next fastest ADMET web server. ADMET-AI can also be run locally with predictions for one million molecules taking just 3.1 hours. Availability and Implementation The ADMET-AI platform is freely available both as a web server at admet.ai.greenstonebio.com and as an open-source Python package for local batch prediction at github.com/swansonk14/admet_ai (also archived on Zenodo at doi.org/10.5281/zenodo.10372930 ). All data and models are archived on Zenodo at doi.org/10.5281/zenodo.10372418 .
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8
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Bogoyavlenskiy A, Zaitseva I, Alexyuk P, Alexyuk M, Omirtaeva E, Manakbayeva A, Moldakhanov Y, Anarkulova E, Imangazy A, Berezin V, Korulkin D, Hasan AH, Noamaan M, Jamalis J. Naturally Occurring Isorhamnetin Glycosides as Potential Agents Against Influenza Viruses: Antiviral and Molecular Docking Studies. ACS OMEGA 2023; 8:48499-48514. [PMID: 38144046 PMCID: PMC10734298 DOI: 10.1021/acsomega.3c08407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023]
Abstract
Influenza remains one of the most widespread infections, causing an annual illness in adults and children. Therefore, the search for new antiviral drugs is one of the priorities of practical health care. Eight isorhamnetin glycosides were purified from Persicaria species, characterized by nuclear magnetic resonance spectroscopy and mass spectrometry and then evaluated as potential agents against influenza virus. A comprehensive in vitro and in vivo assessment of the compounds revealed that compound 5 displayed the most potent inhibitory activity with an EC50 value of 1.2-1.3 μM, better than standard drugs (isorhamnetin 28.0-56.0 μM and oseltamivir 1.3-9.1 μM). Molecular docking results also revealed that compound 5 has the lowest binding energy (-10.7 kcal/mol) among the tested compounds and isorhamnetin (-8.1 kcal/mol). The ability of the isorhamnetin glycosides to suppress the reproduction of the influenza virus was studied on a model of a cell culture and chicken embryos. The ability of active compounds to influence the structure of the virion, as well as the activity of hemagglutinin and neuraminidase, has been demonstrated. Compound 1, 5, and 6 demonstrated the most effective inhibition of virus replication for all tested viruses. Molecular dynamics simulation techniques were run for 100 ns for compound 5 with two protein receptors Hem (1RUY) and Neu (3BEQ). These results revealed that the Hem-complex system acquired a relatively more stable conformation and even better descriptors than the other Neu-complex studied systems, suggesting that it can be an effective inhibiting drug toward hemagglutinin than neuraminidase inhibition. Based on the reported results, compound 5 can be a good candidate to be evaluated for effectiveness in preclinical testing.
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Affiliation(s)
- Andrey Bogoyavlenskiy
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Irina Zaitseva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Pavel Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Elmira Omirtaeva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Adolat Manakbayeva
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Yergali Moldakhanov
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Elmira Anarkulova
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Anar Imangazy
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Research
and Production Center for Microbiology and Virology, Almaty 050010, Kazakhstan
| | - Dmitry Korulkin
- Department
of Chemistry and Chemical Technology, al-Farabi
Kazakh National University, Almaty 050010, Kazakhstan
| | - Aso Hameed Hasan
- Department
of Chemistry, College of Science, University
of Garmian, Kalar, Kurdistan Region 46021, Iraq
| | - Mahmoud Noamaan
- Mathematics
Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Joazaizulfazli Jamalis
- Department
of Chemistry Faculty of Science, Universiti
Teknologi Malaysia, UTM Johor
Bahru, Johor 81310, Malaysia
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9
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Almalki AA, Shafie A, Hazazi A, Banjer HJ, Bakhuraysah MM, Almaghrabi SA, Alsaiari AA, Alsaeedi FA, Ashour AA, Alharthi A, Alharthi NS, Anjum F. Targeting Cathepsin L in Cancer Management: Leveraging Machine Learning, Structure-Based Virtual Screening, and Molecular Dynamics Studies. Int J Mol Sci 2023; 24:17208. [PMID: 38139037 PMCID: PMC10743089 DOI: 10.3390/ijms242417208] [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: 11/15/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Cathepsin L (CTSL) expression is dysregulated in a variety of cancers. Extensive empirical evidence indicates their direct participation in cancer growth, angiogenic processes, metastatic dissemination, and the development of treatment resistance. Currently, no natural CTSL inhibitors are approved for clinical use. Consequently, the development of novel CTSL inhibition strategies is an urgent necessity. In this study, a combined machine learning (ML) and structure-based virtual screening strategy was employed to identify potential natural CTSL inhibitors. The random forest ML model was trained on IC50 values. The accuracy of the trained model was over 90%. Furthermore, we used this ML model to screen the Biopurify and Targetmol natural compound libraries, yielding 149 hits with prediction scores >0.6. These hits were subsequently selected for virtual screening using a structure-based approach, yielding 13 hits with higher binding affinity compared to the positive control (AZ12878478). Two of these hits, ZINC4097985 and ZINC4098355, have been shown to strongly bind CTSL proteins. In addition to drug-like properties, both compounds demonstrated high affinity, ligand efficiency, and specificity for the CTSL binding pocket. Furthermore, in molecular dynamics simulations spanning 200 ns, these compounds formed stable protein-ligand complexes. ZINC4097985 and ZINC4098355 can be considered promising candidates for CTSL inhibition after experimental validation, with the potential to provide therapeutic benefits in cancer management.
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Affiliation(s)
- Abdulraheem Ali Almalki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia;
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Maha M. Bakhuraysah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Sarah Abdullah Almaghrabi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Center of Innovations in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Fouzeyyah Ali Alsaeedi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif 21944, Saudi Arabia;
| | - Afaf Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
| | - Nahed S. Alharthi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (A.S.); (H.J.B.); (M.M.B.); (A.A.A.); (F.A.A.); (A.A.)
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10
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Lv Q, Zhou F, Liu X, Zhi L. Artificial intelligence in small molecule drug discovery from 2018 to 2023: Does it really work? Bioorg Chem 2023; 141:106894. [PMID: 37776682 DOI: 10.1016/j.bioorg.2023.106894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Utilizing artificial intelligence (AI) in drug design represents an advanced approach for identifying targets and developing new drugs. Integrating AI techniques significantly reduces the workload involved in drug development and enhances the efficiency of early-stage drug discovery. This review aims to present a comprehensive overview of the utilization of AI methods in the field of small drug design, with a specific focus on four key areas: protein structure prediction, molecular virtual screening, molecular design, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction. Additionally, the role and limitations of AI in drug development are explored, and the impact of AI on decision-making processes is studied. It is important to note that while AI can bring numerous benefits to the early stage of drug development, the direction and quality of decision-making should still be emphasized, as AI should be considered as a tool rather than a decisive factor.
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Affiliation(s)
- Qi Lv
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, PR China
| | - Feilong Zhou
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, PR China
| | - Xinhua Liu
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, PR China.
| | - Liping Zhi
- School of Health Management, Anhui Medical University Hefei, 230032, PR China.
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11
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Sakhawat A, Khan MU, Rehman R, Khan S, Shan MA, Batool A, Javed MA, Ali Q. Natural compound targeting BDNF V66M variant: insights from in silico docking and molecular analysis. AMB Express 2023; 13:134. [PMID: 38015338 PMCID: PMC10684480 DOI: 10.1186/s13568-023-01640-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Brain-Derived Neurotrophic Factor (BDNF) is a neurotrophin gene family gene that encodes proteins vital for the growth, maintenance, and survival of neurons in the nervous system. The study aimed to screen natural compounds against BDNF variant (V66M), which affects memory, cognition, and mood regulation. BDNF variant (V66M) as a target structure was selected, and Vitamin D, Curcumin, Vitamin C, and Quercetin as ligands structures were taken from PubChem database. Multiple tools like AUTODOCK VINA, BIOVIA discovery studio, PyMOL, CB-dock, IMOD server, Swiss ADEMT, and Swiss predict ligands target were used to analyze binding energy, interaction, stability, toxicity, and visualize BDNF-ligand complexes. Compounds Vitamin D3, Curcumin, Vitamin C, and Quercetin with binding energies values of - 5.5, - 6.1, - 4.5, and - 6.7 kj/mol, respectively, were selected. The ligands bind to the active sites of the BDNF variant (V66M) via hydrophobic bonds, hydrogen bonds, and electrostatic interactions. Furthermore, ADMET analysis of the ligands revealed they exhibited sound pharmacokinetic and toxicity profiles. In addition, an MD simulation study showed that the most active ligand bound favorably and dynamically to the target protein, and protein-ligand complex stability was determined. The finding of this research could provide an excellent platform for discovering and rationalizing novel drugs against stress related to BDNF (V66M). Docking, preclinical drug testing and MD simulation results suggest Quercetin as a more potent BDNF variant (V66M) inhibitor and forming a more structurally stable complex.
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Affiliation(s)
- Azra Sakhawat
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
| | - Raima Rehman
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Samiullah Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Adnan Shan
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Alia Batool
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
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12
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Yue Y, Fang Y, Jia R, Cao K, Chen X, Xia H, Cheng Z. Study on the Antioxidant Effect of Shikonin-Loaded β-Cyclodextrin Forming Host-Guest Complexes That Prevent Skin from Photoaging. Int J Mol Sci 2023; 24:15177. [PMID: 37894857 PMCID: PMC10607292 DOI: 10.3390/ijms242015177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
When the skin is overexposed to ultraviolet rays, free radicals will accumulate in the skin, causing lipid damage and even inducing photoaging of the skin. Combination therapy with antioxidant drugs is a good choice for topical treatment of skin photoaging due to its special physiological structure. In this paper, shikonin was encapsulated in β-cyclodextrin (SH-β-CD) by the precipitation crystallization method, which delayed the release of the drug and increased drug solubility. The average diameter of SH-β-CD was 203.0 ± 21.27 nm with a zeta potential of -14.4 ± 0.5 mV. The encapsulation efficiency (EE%) was 65.9 ± 7.13%. The results of the in vitro permeation across the dialysis membrane and ex vivo transdermal release rates were 52.98 ± 1.21% and 88.25 ± 3.26%, respectively. In vitro antioxidant and antilipid peroxidation model assay revealed the antioxidant potential of SH and SH-β-CD. In the mice model of skin photoaging, SH and SH-β-CD had a recovery effect on the skin damage of mice, which could significantly increase the superoxide dismutase (SOD) activity in the skin. Briefly, SH-β-CD had an obvious therapeutic effect on the skin photoaging of mice caused by UV, and it is promising in skin disease treatment and skin care.
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Affiliation(s)
| | | | | | | | | | - Hongmei Xia
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; (Y.Y.); (Y.F.); (R.J.); (K.C.); (X.C.); (Z.C.)
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13
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Garcia PJB, Huang SKH, De Castro-Cruz KA, Leron RB, Tsai PW. In Silico Neuroprotective Effects of Specific Rheum palmatum Metabolites on Parkinson's Disease Targets. Int J Mol Sci 2023; 24:13929. [PMID: 37762232 PMCID: PMC10530814 DOI: 10.3390/ijms241813929] [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: 07/16/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Parkinson's disease (PD) is one of the large-scale health issues detrimental to human quality of life, and current treatments are only focused on neuroprotection and easing symptoms. This study evaluated in silico binding activity and estimated the stability of major metabolites in the roots of R. palmatum (RP) with main protein targets in Parkinson's disease and their ADMET properties. The major metabolites of RP were subjected to molecular docking and QSAR with α-synuclein, monoamine oxidase isoform B, catechol o-methyltransferase, and A2A adenosine receptor. From this, emodin had the greatest binding activity with Parkinson's disease targets. The chemical stability of the selected compounds was estimated using density functional theory analyses. The docked compounds showed good stability for inhibitory action compared to dopamine and levodopa. According to their structure-activity relationship, aloe-emodin, chrysophanol, emodin, and rhein exhibited good inhibitory activity to specific targets. Finally, mediocre pharmacokinetic properties were observed due to unexceptional blood-brain barrier penetration and safety profile. It was revealed that the major metabolites of RP may have good neuroprotective activity as an additional hit for PD drug development. Also, an association between redox-mediating and activities with PD-relevant protein targets was observed, potentially opening discussion on electrochemical mechanisms with biological functions.
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Affiliation(s)
- Patrick Jay B. Garcia
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines; (P.J.B.G.); (K.A.D.C.-C.); (R.B.L.)
- School of Graduate Studies, Mapúa University, Manila 1002, Philippines
| | - Steven Kuan-Hua Huang
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan;
- Division of Urology, Department of Surgery, Chi Mei Medical Center, Tainan 711, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Kathlia A. De Castro-Cruz
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines; (P.J.B.G.); (K.A.D.C.-C.); (R.B.L.)
| | - Rhoda B. Leron
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Manila 1002, Philippines; (P.J.B.G.); (K.A.D.C.-C.); (R.B.L.)
| | - Po-Wei Tsai
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan;
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14
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Kaur A, Goyal B. In silico design and identification of new peptides for mitigating hIAPP aggregation in type 2 diabetes. J Biomol Struct Dyn 2023:1-16. [PMID: 37691445 DOI: 10.1080/07391102.2023.2254411] [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: 05/10/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
The aberrant misfolding and self-aggregation of human islet amyloid polypeptide (hIAPP or amylin) into cytotoxic aggregates are implicated in the pathogenesis of type 2 diabetes (T2D). Among various inhibitors, short peptides derived from the amyloidogenic regions of hIAPP have been employed as hIAPP aggregation inhibitors due to their low immunogenicity, biocompatibility, and high chemical diversity. Recently, hIAPP fragment HSSNN18-22 was identified as an amyloidogenic sequence and displayed higher antiproliferative activity to RIN-5F cells. Various hIAPP aggregation inhibitors have been designed by chemical modifications of the highly amyloidogenic sequence (NFGAIL) of hIAPP. In this work, a library of pentapeptides based on fragment HSSNN18-22 was designed and assessed for their efficacy in blocking hIAPP aggregation using an integrated computational screening approach. The binding free energy calculations by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method identified HSSQN and HSSNQ that bind to hIAPP monomer with a binding affinity of -21.25 ± 4.90 and -19.73 ± 3.10 kcal/mol, respectively, which is notably higher as compared to HSSNN (-11.90 ± 4.12 kcal/mol). The sampling of the non aggregation-prone helical conformation was notably increased from 23.5 ± 3.0 in the hIAPP monomer to 38.1 ± 3.6, and 33.8 ± 3.0% on the incorporation of HSSQN, and HSSNQ, respectively, which indicate reduced aggregation propensity of hIAPP monomer. The pentapeptides, HSSQN and HSSNQ, identified as hIAPP aggregation inhibitors in this work can be further conjugated with various metal chelating peptides to yield more efficacious and clinically relevant multifunctional modulators for targeting various pathological hallmarks of T2D.
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Affiliation(s)
- Apneet Kaur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, India
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15
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Vangala SR, Krishnan SR, Bung N, Srinivasan R, Roy A. pBRICS: A Novel Fragmentation Method for Explainable Property Prediction of Drug-Like Small Molecules. J Chem Inf Model 2023; 63:5066-5076. [PMID: 37585609 DOI: 10.1021/acs.jcim.3c00689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Generative artificial intelligence algorithms have shown to be successful in exploring large chemical spaces and designing novel and diverse molecules. There has been considerable interest in developing predictive models using artificial intelligence for drug-like properties, which can potentially reduce the late-stage attrition of drug candidates or predict the properties of novel AI-designed molecules. Concurrently, it is important to understand the contribution of functional groups toward these properties and modify them to obtain property-optimized lead compounds. As a result, there is an increasing interest in the development of explainable property prediction models. However, current explainable approaches are mostly atom-based, where, often, only a fraction of a fragment is shown to be significant. To address the above challenges, we have developed a novel domain-aware molecular fragmentation approach termed post-processing of BRICS (pBRICS), which can fragment small molecules into their functional groups. Multitask models were developed to predict various properties, including the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. The fragment importance was explained using the gradient-weighted class activation mapping (Grad-CAM) approach. The method was validated on data sets of experimentally available matched molecular pairs (MMPs). The explanations from the model can be useful for medicinal chemists to identify the fragments responsible for poor drug-like properties and optimize the molecule. The explainability approach was also used to identify the reason behind false positive and false negative MMP predictions. Based on evidence from the existing literature and our analysis, some of these mispredictions were justified. We propose that the quantity, quality, and diversity of the training data will improve the accuracy of property prediction algorithms for novel molecules.
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Affiliation(s)
- Sarveswara Rao Vangala
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India
| | | | - Navneet Bung
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India
| | - Rajgopal Srinivasan
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India
| | - Arijit Roy
- TCS Research (Life Sciences Division), Tata Consultancy Services Limited, Hyderabad 500081, India
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16
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Hagg A, Kirschner KN. Open-Source Machine Learning in Computational Chemistry. J Chem Inf Model 2023; 63:4505-4532. [PMID: 37466636 PMCID: PMC10430767 DOI: 10.1021/acs.jcim.3c00643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Indexed: 07/20/2023]
Abstract
The field of computational chemistry has seen a significant increase in the integration of machine learning concepts and algorithms. In this Perspective, we surveyed 179 open-source software projects, with corresponding peer-reviewed papers published within the last 5 years, to better understand the topics within the field being investigated by machine learning approaches. For each project, we provide a short description, the link to the code, the accompanying license type, and whether the training data and resulting models are made publicly available. Based on those deposited in GitHub repositories, the most popular employed Python libraries are identified. We hope that this survey will serve as a resource to learn about machine learning or specific architectures thereof by identifying accessible codes with accompanying papers on a topic basis. To this end, we also include computational chemistry open-source software for generating training data and fundamental Python libraries for machine learning. Based on our observations and considering the three pillars of collaborative machine learning work, open data, open source (code), and open models, we provide some suggestions to the community.
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Affiliation(s)
- Alexander Hagg
- Institute
of Technology, Resource and Energy-Efficient Engineering (TREE), University of Applied Sciences Bonn-Rhein-Sieg, 53757 Sankt Augustin, Germany
- Department
of Electrical Engineering, Mechanical Engineering and Technical Journalism, University of Applied Sciences Bonn-Rhein-Sieg, 53757 Sankt Augustin, Germany
| | - Karl N. Kirschner
- Institute
of Technology, Resource and Energy-Efficient Engineering (TREE), University of Applied Sciences Bonn-Rhein-Sieg, 53757 Sankt Augustin, Germany
- Department
of Computer Science, University of Applied
Sciences Bonn-Rhein-Sieg, 53757 Sankt Augustin, Germany
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17
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Ketkar R, Liu Y, Wang H, Tian H. A Benchmark Study of Graph Models for Molecular Acute Toxicity Prediction. Int J Mol Sci 2023; 24:11966. [PMID: 37569341 PMCID: PMC10418346 DOI: 10.3390/ijms241511966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
With the wide usage of organic compounds, the assessment of their acute toxicity has drawn great attention to reduce animal testing and human labor. The development of graph models provides new opportunities for acute toxicity prediction. In this study, five graph models (message-passing neural network, graph convolution network, graph attention network, path-augmented graph transformer network, and Attentive FP) were applied on four toxicity tasks (fish, Daphnia magna, Tetrahymena pyriformis, and Vibrio fischeri). With the lowest prediction error, Attentive FP was reported to have the best performance in all four tasks. Moreover, the attention weights of the Attentive FP model helped to construct atomic heatmaps and provide good explainability.
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Affiliation(s)
- Rajas Ketkar
- Yale College, Yale University, New Haven, CT 06520, USA
| | - Yue Liu
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Hengji Wang
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Hao Tian
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA
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18
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Hakeem IJ. Molecular docking analysis of acetylcholinesterase inhibitors for Alzheimer's disease management. Bioinformation 2023; 19:565-570. [PMID: 37886145 PMCID: PMC10599677 DOI: 10.6026/97320630019565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 10/28/2023] Open
Abstract
Alzheimer's disease (AD) is a neurological disease that is related to aging and is the leading cause of dementia globally. AD has a significant influence on cognitive functions, particularly memory, resulting in a variety of functional deficits. Given the increasing prevalence of AD, there is an urgent need for the development of effective therapeutic therapies. In a quest to uncover a holistic remedy for AD, a total of 41 bioactive compounds derived from three distinct medicinal plant sources were screened to evaluate their potential to inhibit the active sites of acetylcholinesterase (AChE). The insilico screening protocol included 24 licorice-derived compounds, 5 ginkgo biloba-derived compounds, and 11 ginseng-derived compounds. Two compounds (Ginkgolide A and Licorice glycoside D2) were observed to display greater binding energy (BE) relative to the control by interacting with crucial residues in the active site of AChE. Ginkgolide A and Licorice glycoside D2 exhibited BEs of -11.3 and -11.2 kcal/mol, respectively, whereas the control, Donepezil, demonstrated a BE of -10.8 kcal/mol. Further, these compounds exhibit favorable drug-likeness properties. This study suggests that further experimental investigations can be conducted on Ginkgolide A and Licorice glycoside D2 to explore their potential therapeutic applications for AD.
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Affiliation(s)
- Israa J Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
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19
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J. Hakeem I, Alsharif FH, Aljadani M, Fahad Alabbas I, Faqihi MS, Aloufi AH, Almutairi WA, Akber AH, Alam Q. Molecular docking analysis of KRAS inhibitors for cancer management. Bioinformation 2023; 19:411-416. [PMID: 37822837 PMCID: PMC10563554 DOI: 10.6026/97320630019411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 10/13/2023] Open
Abstract
The majority of human tumors are characterized by abnormal signaling caused by oncogenic RAS proteins. KRAS is a member of the RAS family and is currently one of the most thoroughly researched targets for cancer treatment due to its prevalence in a variety of deadly malignancies. Targeting the KRAS protein, which plays a crucial role in regulating cell growth, differentiation, and apoptosis, shows great potential as a strategy for fighting cancer. Herein, in silico screening of 530 natural compounds against KRAS protein was performed. The top-scoring hits, namely ZINC32502206, ZINC98363763, ZINC85645815, and ZINC98364259 displayed a robust affinity towards KRAS as evidenced by their respective binding affinity values of -10.50, -10.01, -9.80, and -9.70 kcal/mol, respectively which were notably higher than that of the control compound AMG 510 (-9.10 kcal/mol). Through virtual screening and visual inspection, it was observed that these hits effectively interacted with the essential residues located within the active site of KRAS. Based on the findings of this study, it can be inferred that these compounds may have the potential to be employed in the treatment of cancer by targeting KRAS.
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Affiliation(s)
- Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatmah Hazza Alsharif
- Department of Medical Surgical Nursing Oncology and Palliative Care Nursing, Faculty of Nursing, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majidah Aljadani
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Ibrahim Fahad Alabbas
- Central Military Laboratory and Blood Bank Department - Virology Division, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Mohammed Saud Faqihi
- Central Military Laboratory and Blood Bank Department - Microbiology Division, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Ahmed Hamdan Aloufi
- Department of Pathology and Laboratory Medicine, Imam Abdulrahman bin Faisal Hospital Ministry of National Guard Health Affairs, P.O. Box 34232 Dhahran, Saudi Arabia
| | - Wael Abdullah Almutairi
- Department of Respiratory Services, Ministry of National Guard Hospital and Health Affairs (MNGHA) P.O. box 22490, kingdom of Saudi Arabia
| | - Asif Hussain Akber
- Central Military Laboratory and Blood Bank Department - Virology Division, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Qamre Alam
- Molecular Genomics and Precision Medicine Department, ExpressMed laboratories, Block, 359, Zinj, Kingdom of Bahrain
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Mollineda-Diogo N, Chaviano-Montes de Oca CS, Sifontes-Rodríguez S, Espinosa-Buitrago T, Monzote-Fidalgo L, Meneses-Marcel A, Morales-Helguera A, Perez-Castillo Y, Arán-Redó V. Antileishmanial activity of 5-nitroindazole derivatives. Ther Adv Infect Dis 2023; 10:20499361231208294. [PMID: 37915499 PMCID: PMC10617274 DOI: 10.1177/20499361231208294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/01/2023] [Indexed: 11/03/2023] Open
Abstract
Background Currently, there is no safe and effective vaccine against leishmaniasis and existing therapies are inadequate due to high toxicity, cost and decreased efficacy caused by the emergence of resistant parasite strains. Some indazole derivatives have shown in vitro and in vivo activity against Trichomonas vaginalis and Trypanosoma cruzi. On that basis, 20 indazole derivatives were tested in vitro against Leishmania amazonensis. Objective To evaluate the in vitro activity of twenty 2-benzyl-5-nitroindazolin-3-one derivatives against L. amazonensis. Design For the selection of promising compounds, it is necessary to evaluate the indicators for in vitro activity. For this aim, a battery of studies for antileishmanial activity and cytotoxicity were implemented. These results enabled the determination of the substituents in the indazole derivatives responsible for activity and selectivity, through the analysis of the structure-activity relationship (SAR). Methods In vitro cytotoxicity against mouse peritoneal macrophages and growth inhibitory activity in promastigotes were evaluated for 20 compounds. Compounds that showed adequate selectivity were tested against intracellular amastigotes. The SAR from the results in promastigotes was represented using the SARANEA software. Results Eight compounds showed selectivity index >10% and 50% inhibitory concentration <1 µM against the promastigote stage. Against intracellular amastigotes, four were as active as Amphotericin B. The best results were obtained for 2-(benzyl-2,3-dihydro-5-nitro-3-oxoindazol-1-yl) ethyl acetate, with 50% inhibitory concentration of 0.46 ± 0.01 µM against amastigotes and a selectivity index of 875. The SAR study showed the positive effect on the selectivity of the hydrophilic fragments substituted in position 1 of 2-benzyl-5- nitroindazolin-3-one, which played a key role in improving the selectivity profile of this series of compounds. Conclusion 2-bencyl-5-nitroindazolin-3-one derivatives showed selective and potent in vitro activity, supporting further investigations on this family of compounds as potential antileishmanial hits.
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Affiliation(s)
- Niurka Mollineda-Diogo
- Universidad Central “Marta Abreu” de Las Villas, Centro de Bioactivos Químicos, Carretera a Camajuaní Km. 5 ½, Santa Clara, Villa Clara, Cuba
| | | | - Sergio Sifontes-Rodríguez
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México, México
| | - Teresa Espinosa-Buitrago
- Facultad de Farmacia, Departamento de Parasitología, Universidad Complutense de Madrid, Madrid, España
| | - Lianet Monzote-Fidalgo
- Instituto de Medicina Tropical “Pedro Kourí” (IPK), Departamento de Parasitología, La Habana, Cuba
| | - Alfredo Meneses-Marcel
- Universidad Central “Marta Abreu” de Las Villas, Centro de Bioactivos Químicos, Villa Clara, Cuba
| | - Aliuska Morales-Helguera
- Universidad Central “Marta Abreu” de Las Villas, Centro de Bioactivos Químicos, Villa Clara, Cuba
| | - Yunierkis Perez-Castillo
- Grupo de Bio-Quimioinformática and Área de Ciencias Aplicadas, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, CP 170125, Ecuador
| | - Vicente Arán-Redó
- Instituto de Química Médica del Consejo Superior de Investigaciones Científicas de España, Madrid, España
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