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R D, S W, D P D, R S. Cracking a cancer code DNA methylation in epigenetic modification: an in-silico approach on efficacy assessment of Sri Lanka-oriented nutraceuticals. J Biomol Struct Dyn 2024:1-21. [PMID: 38425013 DOI: 10.1080/07391102.2024.2321235] [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: 08/02/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
DNA methyltransferase (DNMTs) are essential epigenetic modifiers that play a critical role in gene regulation. These enzymes add a methyl group to cytosine's 5'-carbon, specifically within CpG dinucleotides, using S-adenosyl-L-methionine. Abnormal overexpression of DNMTs can alter the gene expression patterns and contribute to cancer development in the human body. Therefore, the inhibition of DNMT is a promising therapeutic approach to cancer treatment. This study was aimed to identify potential nutraceutical inhibitors from the Sri Lanka Flora database using computational methods, which provided an atomic-level description of the drug binding site and examined the interactions between nutraceuticals and amino acids of the DNMT enzyme. A series of nutraceuticals from Sri Lanka-oriented plants were selected and evaluated to assess their inhibitory effects on DNMT using absorption, distribution, metabolism, excretion and toxicity analysis, virtual screening, molecular docking, molecular dynamics simulation and trajectory analysis. Azacitidine, a DNMT inhibitor approved by the US Food and Drug Administration, was selected as a reference inhibitor. The complexes with more negative binding energies were selected and further assessed for their potency. Seven molecules were identified from 200 nutraceuticals, demonstrating significantly negative binding energies against the DNMT enzyme. Various trajectory analyses were conducted to investigate the stability of the DNMT enzyme. The results indicated that petchicine (NP#0003), ouregidione (NP#0011) and azacitidine increased the stability of the DNMT enzyme. Consequently, these two nutraceuticals showed inhibitory efficacies similar to azacitidine, making them potential candidates for therapeutic interventions targeting DNMT enzyme-related cancers. Additional bioassay testing is recommended to confirm the efficacies of these nutraceuticals and explore their applicability in clinical treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dushanan R
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Weerasinghe S
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Dissanayake D P
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Senthilnithy R
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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52
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Draper MR, Waterman A, Dannatt JE, Patel P. Integrating multiscale and machine learning approaches towards the SAMPL9 log P challenge. Phys Chem Chem Phys 2024; 26:7907-7919. [PMID: 38376855 PMCID: PMC10938873 DOI: 10.1039/d3cp04140a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The partition coefficient (log P) is an important physicochemical property that provides information regarding a molecule's pharmacokinetics, toxicity, and bioavailability. Methods to accurately predict the partition coefficient have the potential to accelerate drug design. In an effort to test current methods and explore new computational techniques, the statistical assessment of the modeling of proteins and ligands (SAMPL) has established a blind prediction challenge. The ninth iteration challenge was to predict the toluene-water partition coefficient (log Ptol/w) of sixteen drug molecules. Herein, three approaches are reported broadly under the categories of quantum mechanics (QM), molecular mechanics (MM), and data-driven machine learning (ML). The three blind submissions yield mean unsigned errors (MUE) ranging from 1.53-2.93 log Ptol/w units. The MUEs were reduced to 1.00 log Ptol/w for the QM methods. While MM and ML methods outperformed DFT approaches for challenge molecules with fewer rotational degrees of freedom, they suffered for the larger molecules in this dataset. Overall, DFT functionals paired with a triple-ζ basis set were the simplest and most effective tool to obtain quantitatively accurate partition coefficients.
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Affiliation(s)
- Michael R Draper
- Chemistry Department, University of Dallas, Irving, Texas, 75062, USA.
| | - Asa Waterman
- Chemistry Department, University of Dallas, Irving, Texas, 75062, USA.
| | | | - Prajay Patel
- Chemistry Department, University of Dallas, Irving, Texas, 75062, USA.
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53
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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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54
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Uddin MJ, Niloy SI, Aktaruzzaman M, Talukder MEK, Rahman MM, Imon RR, Uddin AFMS, Amin MZ. Neuropharmacological assessment and identification of possible lead compound (apomorphine) from Hygrophila spinosa through in-vivo and in-silico approaches. J Biomol Struct Dyn 2024:1-16. [PMID: 38385482 DOI: 10.1080/07391102.2024.2317974] [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: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The aim of this research is to examine possible neurological activity of methanol, ethyl acetate, and aqueous extracts of Hygrophila spinosa and identify possible lead compounds through in silico analysis. In vivo, neuropharmacological activity was evaluated by using four distinct neuropharmacological assessment assays. Previously reported GC-MS data and earlier literature were utilized to identify the phytochemicals present in Hygrophila spinosa. Computational studies notably molecular docking and molecular dynamic simulations were conducted with responsible receptors to assess the stability of the best interacting compound. Pharmacokinetics properties like absorption, distribution, metabolism, excretion, and toxicity were considered to evaluate the drug likeliness properties of the identified compounds. All the in vivo results support the notion that different extracts (methanol, ethyl acetate, and aqueous) of Hygrophila spinosa have significant (*p = 0.05) sedative-hypnotic, anxiolytic, and anti-depressant activity. Among all the extracts, specifically methanol extracts of Hygrophila spinosa (MHS 400 mg/kg.b.w.) showed better sedative, anxiolytic and antidepressant activity than aqueous and ethyl acetate extracts. In silico molecular docking analysis revealed that among 53 compounds 7 compounds showed good binding affinities and one compound, namely apomorphine (CID: 6005), surprisingly showed promising binding affinity to all the receptors . An analysis of molecular dynamics simulations confirmed that apomorphine (CID: 6005) had a high level of stability at the protein binding site. Evidence suggests that Hygrophila spinosa has significant sedative, anxiolytic, and antidepressant activity. In silico analysis revealed that a particular compound (apomorphine) is responsible for this action. Further research is required in order to establish apomorphine as a drug for anxiety, depression, and sleep disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Jashim Uddin
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Clinical Pharmacy and Pharmacology. Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Md Aktaruzzaman
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Clinical Pharmacy and Pharmacology. Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Enamul Kabir Talukder
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Mashiar Rahman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Raihan Rahman Imon
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - A F M Shahab Uddin
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Ziaul Amin
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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Mondal I, Halder AK, Pattanayak N, Mandal SK, Cordeiro MNDS. Shaping the Future of Obesity Treatment: In Silico Multi-Modeling of IP6K1 Inhibitors for Obesity and Metabolic Dysfunction. Pharmaceuticals (Basel) 2024; 17:263. [PMID: 38399478 PMCID: PMC10891520 DOI: 10.3390/ph17020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Recent research has uncovered a promising approach to addressing the growing global health concern of obesity and related disorders. The inhibition of inositol hexakisphosphate kinase 1 (IP6K1) has emerged as a potential therapeutic strategy. This study employs multiple ligand-based in silico modeling techniques to investigate the structural requirements for benzisoxazole derivatives as IP6K1 inhibitors. Firstly, we developed linear 2D Quantitative Structure-Activity Relationship (2D-QSAR) models to ensure both their mechanistic interpretability and predictive accuracy. Then, ligand-based pharmacophore modeling was performed to identify the essential features responsible for the compounds' high activity. To gain insights into the 3D requirements for enhanced potency against the IP6K1 enzyme, we employed multiple alignment techniques to set up 3D-QSAR models. Given the absence of an available X-ray crystal structure for IP6K1, a reliable homology model for the enzyme was developed and structurally validated in order to perform structure-based analyses on the selected dataset compounds. Finally, molecular dynamic simulations, using the docked poses of these compounds, provided further insights. Our findings consistently supported the mechanistic interpretations derived from both ligand-based and structure-based analyses. This study offers valuable guidance on the design of novel IP6K1 inhibitors. Importantly, our work exclusively relies on non-commercial software packages, ensuring accessibility for reproducing the reported models.
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Affiliation(s)
- Ismail Mondal
- Dr. B. C. Roy College of Pharmacy and Allied Health Sciences, Dr. Meghnad Saha Sarani, Bidhannagar, Durgapur 713206, India; (I.M.); (A.K.H.); (N.P.); (S.K.M.)
| | - Amit Kumar Halder
- Dr. B. C. Roy College of Pharmacy and Allied Health Sciences, Dr. Meghnad Saha Sarani, Bidhannagar, Durgapur 713206, India; (I.M.); (A.K.H.); (N.P.); (S.K.M.)
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Nirupam Pattanayak
- Dr. B. C. Roy College of Pharmacy and Allied Health Sciences, Dr. Meghnad Saha Sarani, Bidhannagar, Durgapur 713206, India; (I.M.); (A.K.H.); (N.P.); (S.K.M.)
| | - Sudip Kumar Mandal
- Dr. B. C. Roy College of Pharmacy and Allied Health Sciences, Dr. Meghnad Saha Sarani, Bidhannagar, Durgapur 713206, India; (I.M.); (A.K.H.); (N.P.); (S.K.M.)
| | - Maria Natalia D. S. Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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56
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Zhou N, Zheng C, Tan H, Luo L. Identification of PLK1-PBD Inhibitors from the Library of Marine Natural Products: 3D QSAR Pharmacophore, ADMET, Scaffold Hopping, Molecular Docking, and Molecular Dynamics Study. Mar Drugs 2024; 22:83. [PMID: 38393054 PMCID: PMC10890274 DOI: 10.3390/md22020083] [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: 12/30/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
PLK1 is found to be highly expressed in various types of cancers, but the development of inhibitors for it has been slow. Most inhibitors are still in clinical stages, and many lack the necessary selectivity and anti-tumor effects. This study aimed to create new inhibitors for the PLK1-PBD by focusing on the PBD binding domain, which has the potential for greater selectivity. A 3D QSAR model was developed using a dataset of 112 compounds to evaluate 500 molecules. ADMET prediction was then used to select three molecules with strong drug-like characteristics. Scaffold hopping was employed to reconstruct 98 new compounds with improved drug-like properties and increased activity. Molecular docking was used to compare the efficient compound abbapolin, confirming the high-activity status of [(14S)-14-hydroxy-14-(pyridin-2-yl)tetradecyl]ammonium,[(14S)-15-(2-furyl)-14-hydroxypentadecyl]ammonium and [(14S)-14-hydroxy-14-phenyltetradecyl]ammonium. Molecular dynamics simulations and MMPBSA were conducted to evaluate the stability of the compounds in the presence of proteins. An in-depth analysis of [(14S)-15-(2-furyl)-14-hydroxypentadecyl]ammonium and [(14S)-14-hydroxy-14-phenyltetradecyl]ammonium identified them as potential candidates for PLK1 inhibitors.
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Affiliation(s)
- Nan Zhou
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (N.Z.); (C.Z.); (H.T.)
| | - Chuangze Zheng
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (N.Z.); (C.Z.); (H.T.)
| | - Huiting Tan
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (N.Z.); (C.Z.); (H.T.)
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang 524023, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
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57
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Azevedo PHRDA, Peçanha BRDB, Flores-Junior LAP, Alves TF, Dias LRS, Muri EMF, Lima CHDS. In silico drug repurposing by combining machine learning classification model and molecular dynamics to identify a potential OGT inhibitor. J Biomol Struct Dyn 2024; 42:1417-1428. [PMID: 37054524 DOI: 10.1080/07391102.2023.2199868] [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: 10/20/2022] [Accepted: 04/01/2023] [Indexed: 04/15/2023]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is a unique intracellular post-translational glycosylation at the hydroxyl group of serine or threonine residues in nuclear, cytoplasmic and mitochondrial proteins. The enzyme O-GlcNAc transferase (OGT) is responsible for adding GlcNAc, and anomalies in this process can lead to the development of diseases associated with metabolic imbalance, such as diabetes and cancer. Repurposing approved drugs can be an attractive tool to discover new targets reducing time and costs in the drug design. This work focuses on drug repurposing to OGT targets by virtual screening of FDA-approved drugs through consensus machine learning (ML) models from an imbalanced dataset. We developed a classification model using docking scores and ligand descriptors. The SMOTE approach to resampling the dataset showed excellent statistical values in five of the seven ML algorithms to create models from the training set, with sensitivity, specificity and accuracy over 90% and Matthew's correlation coefficient greater than 0.8. The pose analysis obtained by molecular docking showed only H-bond interaction with the OGT C-Cat domain. The molecular dynamics simulation showed the lack of H-bond interactions with the C- and N-catalytic domains allowed the drug to exit the binding site. Our results showed that the non-steroidal anti-inflammatory celecoxib could be a potentially OGT inhibitor.
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Affiliation(s)
| | | | | | - Tatiana Fialho Alves
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Luiza Rosaria Sousa Dias
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Estela Maris Freitas Muri
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, Brazil
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58
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Adebayo GP, Oduselu GO, Aderohunmu DV, Klika KD, Olasehinde GI, Ajani OO, Adebiyi E. Structure-based design, and development of amidinyl, amidoximyl and hydroxamic acid based organic molecules as novel antimalarial drug candidates. ARAB J CHEM 2024; 17:105573. [PMID: 38283036 PMCID: PMC10810238 DOI: 10.1016/j.arabjc.2023.105573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024] Open
Abstract
Malaria remains a significant global health concern causing numerous fatalities and the emergence of antimalarial drug resistance highlights the urgent need for novel therapeutic options with innovative mechanisms of action and targets. This study aimed to design potential inhibitors of Plasmodium falciparum 6-pyruvoyltetrahydropterin synthase (PfPTPS), synthesize them, and experimentally validate their efficacy as antimalarial agents. A structure-based approach was employed to design a series of novel derivatives, including amidinyl, amidoximyl and hydroxamic acid analogs (1c, 1d, 2b, and 3b), with a focus on their ability to bind to the Zn2+ present in the active site of PfPTPS. The syntheses of these compounds were accomplished through various multi-step synthetic pathways and their structural identities were confirmed using 1H and 13C NMR spectra, mass spectra, and elemental analysis. The compounds were screened for their antiplasmodial activity against the NF54 strain of P. falciparum and in vitro cytotoxicity testing was performed using L-6 cells. The in vivo acute toxicity of the compounds was evaluated in mice. Docking studies of the compounds with the 3D structure of PfPTPS revealed their strong binding affinities, with compound 3b exhibiting notable metal-acceptor interaction with the Zn2+ in the protein binding pocket thereby positioning it as a lead compound for PfPTPS inhibition. The in vitro antiplasmodial studies revealed moderate efficacies against the Pf NF54 strain, particularly compounds 1d and 3b which displayed IC50 < 0.2 μM. No significant cytotoxicity was noted on the L-6 rat cell line. Moreover, in vivo studies suggested that compound 3b exhibited both safety and efficacy in treating rodent malaria. The identified lead compound in this study represents a possible candidate for antimalarial drug development and can be further explored in the search for alternative antifolate drugs to combat the malaria menace.
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Affiliation(s)
- Glory P. Adebayo
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Biological Sciences Department, Covenant University, Ota, Nigeria
| | - Gbolahan O. Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | | | - Karel D. Klika
- NMR Structural Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Grace I. Olasehinde
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Biological Sciences Department, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota 112233, Nigeria
| | - Olayinka O. Ajani
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota 112233, Nigeria
- Department of Chemistry, Covenant University, Covenant University, Km 10 Idiroko Road, P.M.B. 1023 Ota, Ogun State, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota 112233, Nigeria
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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59
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Ugrani S. Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:27-46. [PMID: 38157015 PMCID: PMC10853362 DOI: 10.1007/s00249-023-01695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Transmembrane protease serine 2 (TMPRSS2) is an important drug target due to its role in the infection mechanism of coronaviruses including SARS-CoV-2. Current understanding regarding the molecular mechanisms of known inhibitors and insights required for inhibitor design are limited. This study investigates the effect of inhibitor binding on the intramolecular backbone hydrogen bonds (BHBs) of TMPRSS2 using the concept of hydrogen bond wrapping, which is the phenomenon of stabilization of a hydrogen bond in a solvent environment as a result of being surrounded by non-polar groups. A molecular descriptor which quantifies the extent of wrapping around BHBs is introduced for this. First, virtual screening for TMPRSS2 inhibitors is performed by molecular docking using the program DOCK 6 with a Generalized Born surface area (GBSA) scoring function. The docking results are then analyzed using this descriptor and its relationship to the solvent-accessible surface area term ΔGsa of the GBSA score is demonstrated with machine learning regression and principal component analysis. The effect of binding of the inhibitors camostat, nafamostat, and 4-guanidinobenzoic acid (GBA) on the wrapping of important BHBs in TMPRSS2 is also studied using molecular dynamics. For BHBs with a large increase in wrapping groups due to these inhibitors, the radial distribution function of water revealed that certain residues involved in these BHBs, like Gln438, Asp440, and Ser441, undergo preferential desolvation. The findings offer valuable insights into the mechanisms of these inhibitors and may prove useful in the design of new inhibitors.
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Affiliation(s)
- Suraj Ugrani
- Purdue University, West Lafayette, IN, 47907, USA.
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60
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Oselusi SO, Dube P, Odugbemi AI, Akinyede KA, Ilori TL, Egieyeh E, Sibuyi NR, Meyer M, Madiehe AM, Wyckoff GJ, Egieyeh SA. The role and potential of computer-aided drug discovery strategies in the discovery of novel antimicrobials. Comput Biol Med 2024; 169:107927. [PMID: 38184864 DOI: 10.1016/j.compbiomed.2024.107927] [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: 09/06/2023] [Revised: 12/25/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
Antimicrobial resistance (AMR) has become more of a concern in recent decades, particularly in infections associated with global public health threats. The development of new antibiotics is crucial to ensuring infection control and eradicating AMR. Although drug discovery and development are essential processes in the transformation of a drug candidate from the laboratory to the bedside, they are often very complicated, expensive, and time-consuming. The pharmaceutical sector is continuously innovating strategies to reduce research costs and accelerate the development of new drug candidates. Computer-aided drug discovery (CADD) has emerged as a powerful and promising technology that renews the hope of researchers for the faster identification, design, and development of cheaper, less resource-intensive, and more efficient drug candidates. In this review, we discuss an overview of AMR, the potential, and limitations of CADD in AMR drug discovery, and case studies of the successful application of this technique in the rapid identification of various drug candidates. This review will aid in achieving a better understanding of available CADD techniques in the discovery of novel drug candidates against resistant pathogens and other infectious agents.
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Affiliation(s)
- Samson O Oselusi
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535, South Africa
| | - Phumuzile Dube
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535, South Africa
| | - Adeshina I Odugbemi
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, 7535, South Africa
| | - Kolajo A Akinyede
- Department of Science Technology, Biochemistry Unit, The Federal Polytechnic P.M.B.5351, Ado Ekiti, 360231, Nigeria
| | - Tosin L Ilori
- School of Pharmacy, University of the Western Cape, Bellville, Cape Town, 7535, South Africa
| | - Elizabeth Egieyeh
- School of Pharmacy, University of the Western Cape, Bellville, Cape Town, 7535, South Africa
| | - Nicole Rs Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535, South Africa
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535, South Africa
| | - Abram M Madiehe
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535, South Africa
| | - Gerald J Wyckoff
- School of Pharmacy, Division of Pharmacology and Pharmaceutical Sciences, University of Missouri, Kansas City, MO, 64110-2446, United States
| | - Samuel A Egieyeh
- School of Pharmacy, University of the Western Cape, Bellville, Cape Town, 7535, South Africa.
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61
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Li H, Sun X, Cui W, Xu M, Dong J, Ekundayo BE, Ni D, Rao Z, Guo L, Stahlberg H, Yuan S, Vogel H. Computational drug development for membrane protein targets. Nat Biotechnol 2024; 42:229-242. [PMID: 38361054 DOI: 10.1038/s41587-023-01987-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/13/2023] [Indexed: 02/17/2024]
Abstract
The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learning structure-based design and the evaluation of big data. Recent protein structure predictions based on machine learning tools have delivered surprisingly reliable results for water-soluble and membrane proteins but have limitations for development of drugs that target membrane proteins. Structural transitions of membrane proteins have a central role during transmembrane signaling and are often influenced by therapeutic compounds. Resolving the structural and functional basis of dynamic transmembrane signaling networks, especially within the native membrane or cellular environment, remains a central challenge for drug development. Tackling this challenge will require an interplay between experimental and computational tools, such as super-resolution optical microscopy for quantification of the molecular interactions of cellular signaling networks and their modulation by potential drugs, cryo-electron microscopy for determination of the structural transitions of proteins in native cell membranes and entire cells, and computational tools for data analysis and prediction of the structure and function of cellular signaling networks, as well as generation of promising drug candidates.
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Affiliation(s)
- Haijian Li
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Xiaolin Sun
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Wenqiang Cui
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Marc Xu
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junlin Dong
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Babatunde Edukpe Ekundayo
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Zhili Rao
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Liwei Guo
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Shuguang Yuan
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
| | - Horst Vogel
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
- Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Yssartier T, Liu L, Pardoue S, Le Questel JY, Guérard F, Montavon G, Galland N. In vivo stability of 211At-radiopharmaceuticals: on the impact of halogen bond formation. RSC Med Chem 2024; 15:223-233. [PMID: 38283213 PMCID: PMC10809332 DOI: 10.1039/d3md00579h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024] Open
Abstract
211At, when coupled to a targeting agent, is one of the most promising radionuclides for therapeutic applications. The main labelling approach consists in the formation of astatoaryl compounds, which often show a lack of in vivo stability. The hypothesis that halogen bond (XB) interactions with protein functional groups initiate a deastatination mechanism is investigated through radiochemical experiments and DFT modelling. Several descriptors agree on the known mechanism of iodoaryl substrates dehalogenation by iodothyronine deiodinases, supporting the higher in vivo dehalogenation of N-succinimidyl 3-[211At]astatobenzoate (SAB) conjugates in comparison with their iodinated counterparts. The guanidinium group in 3-[211At]astato-4-guanidinomethylbenzoate (SAGMB) prevents the formation of At-mediated XBs with the selenocysteine active site in iodothyronine deiodinases. The initial step of At-aryl bond dissociation is inhibited, elucidating the better in vivo stability of SAGMB conjugates compared with those of SAB. The impact of astatine's ability to form XB interactions on radiopharmaceutical degradation may not be limited to the case of aryl radiolabeling.
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Affiliation(s)
- Thibault Yssartier
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Lu Liu
- CNRS, IPHC UMR 7178, Université de Strasbourg F-67037 Strasbourg France
| | - Sylvain Pardoue
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | | | - François Guérard
- Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Nantes Université, Université d'Angers F-44000 Nantes France
| | - Gilles Montavon
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Nicolas Galland
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
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63
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Cai H, Shen C, Jian T, Zhang X, Chen T, Han X, Yang Z, Dang W, Hsieh CY, Kang Y, Pan P, Ji X, Song J, Hou T, Deng Y. CarsiDock: a deep learning paradigm for accurate protein-ligand docking and screening based on large-scale pre-training. Chem Sci 2024; 15:1449-1471. [PMID: 38274053 PMCID: PMC10806797 DOI: 10.1039/d3sc05552c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The expertise accumulated in deep neural network-based structure prediction has been widely transferred to the field of protein-ligand binding pose prediction, thus leading to the emergence of a variety of deep learning-guided docking models for predicting protein-ligand binding poses without relying on heavy sampling. However, their prediction accuracy and applicability are still far from satisfactory, partially due to the lack of protein-ligand binding complex data. To this end, we create a large-scale complex dataset containing ∼9 M protein-ligand docking complexes for pre-training, and propose CarsiDock, the first deep learning-guided docking approach that leverages pre-training of millions of predicted protein-ligand complexes. CarsiDock contains two main stages, i.e., a deep learning model for the prediction of protein-ligand atomic distance matrices, and a translation, rotation and torsion-guided geometry optimization procedure to reconstruct the matrices into a credible binding pose. The pre-training and multiple innovative architectural designs facilitate the dramatically improved docking accuracy of our approach over the baselines in terms of multiple docking scenarios, thereby contributing to its outstanding early recognition performance in several retrospective virtual screening campaigns. Further explorations demonstrate that CarsiDock can not only guarantee the topological reliability of the binding poses but also successfully reproduce the crucial interactions in crystalized structures, highlighting its superior applicability.
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Affiliation(s)
- Heng Cai
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
| | - Chao Shen
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University Hangzhou 310058 Zhejiang China
| | - Tianye Jian
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University Hangzhou 310058 Zhejiang China
| | - Tong Chen
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
| | - Xiaoqi Han
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
| | - Zhuo Yang
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
| | - Wei Dang
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
| | - Chang-Yu Hsieh
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University Hangzhou 310058 Zhejiang China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University Hangzhou 310058 Zhejiang China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University Hangzhou 310058 Zhejiang China
| | - Xiangyang Ji
- Department of Automation, Tsinghua University Beijing 100084 China
| | - Jianfei Song
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
| | - Tingjun Hou
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University Hangzhou 310058 Zhejiang China
| | - Yafeng Deng
- Hangzhou Carbonsilicon AI Technology Co., Ltd Hangzhou 310018 Zhejiang China
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64
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Sinha P, Yadav AK. Repurposing integrase inhibitors against human T-lymphotropic virus type-1: a computational approach. J Biomol Struct Dyn 2024:1-12. [PMID: 38234060 DOI: 10.1080/07391102.2024.2304681] [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: 08/10/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
Adult T-cell Lymphoma (ATL) is caused by the delta retrovirus family member known as Human T-cell Leukaemia Type I (HTLV-1). Due to the unavailability of any cure, the study gained motivation to identify some repurposed drugs against the virus. A quick and accurate method of screening licensed medications for finding a treatment for HTLV-1 is by cheminformatics drug repurposing in order to analyze a dataset of FDA approved integrase antivirals against HTLV-1 infection. To determine how the antiviral medications interacted with the important residues in the HTLV-1 integrase active regions, molecular docking modeling was used. The steady behavior of the ligands inside the active region was then confirmed by molecular dynamics for the probable receptor-drug complexes. Cabotegravir, Raltegravir and Elvitegravir had the best docking scores with the target, indicating that they can tightly bind to the HTLV-1 integrase. Moreover, MD simulation revealed that the Cabotegravir-HTLV-1, Raltegravir-HTLV-1 and Elvitegravir-HTLV-1 interactions were stable. It is obvious that more testing of these medicines in both clinical trials and experimental tests is necessary to demonstrate their efficacy against HTLV-1 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prashasti Sinha
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Anil Kumar Yadav
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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65
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Dangat Y, Freindorf M, Kraka E. Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study. J Am Chem Soc 2024; 146:145-158. [PMID: 38055807 DOI: 10.1021/jacs.3c06397] [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: 12/08/2023]
Abstract
Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.
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Affiliation(s)
- Yuvraj Dangat
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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66
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Zari A, Kurdi LAF, Jaber FA, Alghamdi KMS, Zari TA, Bahieldin A, Hakeem KR, Alnahdi HS, Edris S, Ashraf GM. Investigation and drug design for novel molecules from natural products as inhibitors for controlling multiple myeloma disease using in-silico tools. J Biomol Struct Dyn 2024:1-16. [PMID: 38173181 DOI: 10.1080/07391102.2023.2300409] [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: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 01/05/2024]
Abstract
Multiple myeloma (MM) is a disease that causes plasma cell growth in the bone marrow and immune globulin buildup in blood and urine. Despite recent advances in MM therapy, many still die due to its high mortality rate. A study using computational simulations analyzed 100 natural ingredients from the SANC database to determine if they inhibited the IgH domain, a known cause of multiple myeloma. Natural component Diospyrin inhibited the IgH enzyme with the best binding energy of -10.3 kcal/mol and three carbon-hydrogen bonds, followed by Parviflorone F complex with a binding energy of -10.1 kcal/mol and two conventional-hydrogen bonds. As a result, the Molecular Dynamic simulation was used to test the stability of the two complexes. During the simulation, the Diospyrin molecule dissociated from the protein at roughly 67.5 ns, whereas the Parviflorone F molecule stayed attached to the protein throughout. The latter was the subject of the investigation. The analysis of the production run data revealed that the Parviflorone F molecule exhibits a variety of conformations within the binding pocket while keeping a relatively constant distance from the protein's center of mass. The analysis of the production run data revealed that the Parviflorone F molecule exhibited a variety of conformations within the binding pocket while keeping a relatively constant distance from the protein's center of mass. The root mean square deviation (RMSD) plots for both the protein and complex showed a stable and steady average value of 4.4 Å for the first 82 nanoseconds of manufacture. As a result, the average value increased to 8.3 Å. Furthermore, the components of the binding free energy, as computed by MM-GBSA, revealed that the mean binding energy of the Parviflorone F molecule was -23.88 kcal/mol. Finally, after analyzing all of the examination data, Parviflorone F was identified as a powerful inhibitor of the IgH domain and hence of the MM disease, which requires further in-vivo conformation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Lina A F Kurdi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatima A Jaber
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Khalid M S Alghamdi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Talal A Zari
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Public Health, Daffodil International University, Dhaka, Bangladesh
| | - Hanan S Alnahdi
- Department of Biochemistry, College of Science, University of Jeddah, Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Al Borg Medical Laboratories, Jeddah, Saudi Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences and Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
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67
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Nejabat M, Hadizadeh F, Nejabat M, Rajabi O. Novel hits for autosomal dominated polycystic kidney disease (ADPKD) targeting derived by in silico screening on ZINC-15 natural product database. J Biomol Struct Dyn 2024; 42:885-902. [PMID: 37029756 DOI: 10.1080/07391102.2023.2196700] [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: 11/19/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic kidney disorder that leads to growth cysts in the kidney, ultimately resulting in loss of function. Currently, no effective drug therapy can be safely used in the clinic. So, looking for effective therapeutic drugs is urgent for treating ADPKD. Our natural product library was prepared based on the ZINC-15 database. Lipinski's rule of five, drug-likeness, and toxicity screening of the designed library were evaluated. Swiss model online server was used for modeling of GANAB target. Finally, docking-based screening against ADPKD targets was done by MOE 2019 software. The top 14 favorable druglike and non-toxic hits were selected for docking studies. Our results showed that compound-10 (ZINC 6073947) as a sesquiterpene coumarin had more negative binding interaction into the active site of PPARG, OXSR1, GANAB, AVPR2, and PC2 with docking scores of -8.22, -7.52, -6.98, -6.61 and -6.05 kcal/mol, respectively, in comparison to Curcumin, as a natural product that is now in phase 4 clinical trial in ADPKD disease, with an affinity of -8.03, -6.42, -6.82, -5.84 and -5.10 kcal/mol, respectively. Furthermore, seven sesquiterpene coumarins similar to compound 10 were generated and docked. Farnesiferol B (16), compared to compound-10, showed binding affinity of -8.16, -6.4, -7.46, -6.92, and -6.11 kcal/mol against the above targets, respectively. Molecular dynamics, which was done on the compound-10 and 16 (Farnesiferol B) in complex with PPARG, GANAB, and AVPR2, showed more negative binding free-energy than Pioglitazone, Miglitol, and Tolvaptan as FDA-approved drugs for each target, respectively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mojgan Nejabat
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Masoud Nejabat
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Omid Rajabi
- Department of Pharmaceutical and Food Control, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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68
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Rawat S, Subramaniam K, Subramanian SK, Subbarayan S, Dhanabalan S, Chidambaram SKM, Stalin B, Roy A, Nagaprasad N, Aruna M, Tesfaye JL, Badassa B, Krishnaraj R. Drug Repositioning Using Computer-aided Drug Design (CADD). Curr Pharm Biotechnol 2024; 25:301-312. [PMID: 37605405 DOI: 10.2174/1389201024666230821103601] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/03/2023] [Accepted: 03/20/2023] [Indexed: 08/23/2023]
Abstract
Drug repositioning is a method of using authorized drugs for other unusually complex diseases. Compared to new drug development, this method is fast, low in cost, and effective. Through the use of outstanding bioinformatics tools, such as computer-aided drug design (CADD), computer strategies play a vital role in the re-transformation of drugs. The use of CADD's special strategy for target-based drug reuse is the most promising method, and its realization rate is high. In this review article, we have particularly focused on understanding the various technologies of CADD and the use of computer-aided drug design for target-based drug reuse, taking COVID-19 and cancer as examples. Finally, it is concluded that CADD technology is accelerating the development of repurposed drugs due to its many advantages, and there are many facts to prove that the new ligand-targeting strategy is a beneficial method and that it will gain momentum with the development of technology.
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Affiliation(s)
- Sona Rawat
- School of Life Sciences, Jaipur National University, Jaipur-302017, India
| | - Kanmani Subramaniam
- Department of Civil Engineering, KPR Institute of Engineering and Technology, Coimbatore-641407, Tamil Nadu, India
| | - Selva Kumar Subramanian
- Department of Sciences, Amrita School of Engineering, Coimbatore - 641112, Tamil Nadu, India
| | - Saravanan Subbarayan
- Department of Civil Engineering, National Institute of Technology, Trichy-620015, Tamil Nadu, India
| | - Subramanian Dhanabalan
- Department of Mechanical Engineering, M. Kumarasamy College of Engineering, Karur - 639113, Tamil Nadu, India
| | | | - Balasubramaniam Stalin
- Department of Mechanical Engineering, Anna University, Regional Campus Madurai, Madurai - 625 019, Tamil Nadu, India
| | - Arpita Roy
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida 201310, India
| | - Nagaraj Nagaprasad
- Department of Mechanical Engineering, ULTRA College of Engineering and Technology, Madurai - 625104, Tamilnadu, India
| | - Mahalingam Aruna
- College of Engineering and Computing, Al Ghurair University, Academic City, Dubai, UAE
| | - Jule Leta Tesfaye
- Dambi Dollo University, College of Natural and Computational Science, Department of Physics, Ethiopia
- Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dambi Dollo, Ethiopia
- Ministry of innovation and technology, Ethiopia
| | - Bayissa Badassa
- Department of Mechanical Engineering, Dambi Dollo University, Dambi Dollo, Ethiopia
| | - Ramaswamy Krishnaraj
- Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dambi Dollo, Ethiopia
- Ministry of innovation and technology, Ethiopia
- Department of Mechanical Engineering, Dambi Dollo University, Dambi Dollo, Ethiopia
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69
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Li B, Wang Y, Yin Z, Xu L, Xie L, Xu X. Decision tree-based identification of important molecular fragments for protein-ligand binding. Chem Biol Drug Des 2024; 103:e14427. [PMID: 38230776 DOI: 10.1111/cbdd.14427] [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: 09/26/2023] [Revised: 11/16/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
Fragment-based drug design is an emerging technology in pharmaceutical research and development. One of the key aspects of this technology is the identification and quantitative characterization of molecular fragments. This study presents a strategy for identifying important molecular fragments based on molecular fingerprints and decision tree algorithms and verifies its feasibility in predicting protein-ligand binding affinity. Specifically, the three-dimensional (3D) structures of protein-ligand complexes are encoded using extended-connectivity fingerprints (ECFP), and three decision tree models, namely Random Forest, XGBoost, and LightGBM, are used to quantitatively characterize the feature importance, thereby extracting important molecular fragments with high reliability. Few-shot learning reveals that the extracted molecular fragments contribute significantly and consistently to the binding affinity even with a small sample size. Despite the absence of location and distance information for molecular fragments in ECFP, 3D visualization, in combination with the reverse ECFP process, shows that the majority of the extracted fragments are located at the binding interface of the protein and the ligand. This alignment with the distance constraints critical for binding affinity further supports the reliability of the strategy for identifying important molecular fragments.
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Affiliation(s)
- Baiyi Li
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yunsong Wang
- School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Zuode Yin
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
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70
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Thirunavukkarasu MK, Veerappapillai S, Karuppasamy R. Sequential virtual screening collaborated with machine-learning strategies for the discovery of precise medicine against non-small cell lung cancer. J Biomol Struct Dyn 2024; 42:615-628. [PMID: 36995235 DOI: 10.1080/07391102.2023.2194994] [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: 12/16/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023]
Abstract
Dysregulation of MAPK pathway receptors are crucial in causing uncontrolled cell proliferation in many cancer types including non-small cell lung cancer. Due to the complications in targeting the upstream components, MEK is an appealing target to diminish this pathway activity. Hence, we have aimed to discover potent MEK inhibitors by integrating virtual screening and machine learning-based strategies. Preliminary screening was conducted on 11,808 compounds using the cavity-based pharmacophore model AADDRRR. Further, seven ML models were accessed to predict the MEK active compounds using six molecular representations. The LGB model with morgan2 fingerprints surpasses other models ensuing 0.92 accuracy and 0.83 MCC value versus test set and 0.85 accuracy and 0.70 MCC value with external set. Further, the binding ability of screened hits were examined using glide XP docking and prime-MM/GBSA calculations. Note that we have utilized three ML-based scoring functions to predict the various biological properties of the compounds. The two hit compounds such as DB06920 and DB08010 resulted excellent binding mechanism with acceptable toxicity properties against MEK. Further, 200 ns of MD simulation combined with MM-GBSA/PBSA calculations confirms that DB06920 may have stable binding conformations with MEK thus step forwarded to the experimental studies in the near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muthu Kumar Thirunavukkarasu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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71
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Liu K, Tong J, Liu X, Liang D, Ren F, Jiang N, Hao Z, Li S, Wang Q. The Discovery of Novel Agents against Staphylococcus aureus by Targeting Sortase A: A Combination of Virtual Screening and Experimental Validation. Pharmaceuticals (Basel) 2023; 17:58. [PMID: 38256891 PMCID: PMC11100315 DOI: 10.3390/ph17010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/24/2024] Open
Abstract
Staphylococcus aureus (S. aureus), commonly known as "superbugs", is a highly pathogenic bacterium that poses a serious threat to human health. There is an urgent need to replace traditional antibiotics with novel drugs to combat S. aureus. Sortase A (SrtA) is a crucial transpeptidase involved in the adhesion process of S. aureus. The reduction in virulence and prevention of S. aureus infections have made it a significant target for antimicrobial drugs. In this study, we combined virtual screening with experimental validation to identify potential drug candidates from a drug library. Three hits, referred to as Naldemedine, Telmisartan, and Azilsartan, were identified based on docking binding energy and the ratio of occupied functional sites of SrtA. The stability analysis manifests that Naldemedine and Telmisartan have a higher binding affinity to the hydrophobic pockets. Specifically, Telmisartan forms stable hydrogen bonds with SrtA, resulting in the highest binding energy. Our experiments prove that the efficiency of adhesion and invasion by S. aureus can be decreased without significantly affecting bacterial growth. Our work identifies Telmisartan as the most promising candidate for inhibiting SrtA, which can help combat S. aureus infection.
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Affiliation(s)
- Kang Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Jiangbo Tong
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Xu Liu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225009, China;
| | - Dan Liang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Fangzhe Ren
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Nan Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Zhenyu Hao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Shixin Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Qiang Wang
- Department of the Heart and Great Vessels, Affiliated Hospital of Yangzhou University, Yangzhou 225009, China
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72
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Angelo JS, Guedes IA, Barbosa HJC, Dardenne LE. Multi-and many-objective optimization: present and future in de novo drug design. Front Chem 2023; 11:1288626. [PMID: 38192501 PMCID: PMC10773868 DOI: 10.3389/fchem.2023.1288626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
de novo Drug Design (dnDD) aims to create new molecules that satisfy multiple conflicting objectives. Since several desired properties can be considered in the optimization process, dnDD is naturally categorized as a many-objective optimization problem (ManyOOP), where more than three objectives must be simultaneously optimized. However, a large number of objectives typically pose several challenges that affect the choice and the design of optimization methodologies. Herein, we cover the application of multi- and many-objective optimization methods, particularly those based on Evolutionary Computation and Machine Learning techniques, to enlighten their potential application in dnDD. Additionally, we comprehensively analyze how molecular properties used in the optimization process are applied as either objectives or constraints to the problem. Finally, we discuss future research in many-objective optimization for dnDD, highlighting two important possible impacts: i) its integration with the development of multi-target approaches to accelerate the discovery of innovative and more efficacious drug therapies and ii) its role as a catalyst for new developments in more fundamental and general methodological frameworks in the field.
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Affiliation(s)
| | | | | | - Laurent E. Dardenne
- Coordenação de Modelagem Computacional, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
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73
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Cai L, Wu S, Jia C, Cui C, Sun-Waterhouse D. Active peptides with hypoglycemic effect obtained from hemp (Cannabis sativa L) protein through identification, molecular docking, and virtual screening. Food Chem 2023; 429:136912. [PMID: 37480780 DOI: 10.1016/j.foodchem.2023.136912] [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: 03/31/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Hemp (Cannabis sativa L) seeds are rich in proteins of high nutritional value, which makes the study of beneficial properties of hemp seed proteins and peptides, such as hypotensive and hypoglycemic effects, increasingly attractive. The present results confirm the good processability and stability of the hemp protein hydrolysate obtained by enzymatic hydrolysis of non-dehulled hemp seed meal (NDHM). Six peptides with potential hypoglycemic activity were obtained by ethanol-graded precipitation, Nano LC-Q-Orbitrap-MS/MS mass spectrometry, and computerized virtual screening. Further, validation experiments for in vitro synthesis showed that TGLGR, SPVI, FY, and FR exhibited good α-glucosidase inhibitory activity, respectively. Animal experiments showed that the hemp protein peptides modulated blood glucose and blood lipids in hyperglycemic rats. These results indicate that hemp protein peptides can reduce blood glucose levels in hyperglycemic rats, suggesting that hemp proteins may be a promising natural source for the prevention and treatment of hyperglycemia.
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Affiliation(s)
- Lei Cai
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China
| | - Shengwen Wu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China
| | - Chenggang Jia
- Guilin Sanjin Pharmaceutical Co., Ltd, Guilin 541100, Guangxi, China
| | - Chun Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, Guangdong, China
| | - Dongxiao Sun-Waterhouse
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
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74
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Baselious F, Robaa D, Sippl W. Utilization of AlphaFold models for drug discovery: Feasibility and challenges. Histone deacetylase 11 as a case study. Comput Biol Med 2023; 167:107700. [PMID: 37972533 DOI: 10.1016/j.compbiomed.2023.107700] [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: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Histone deacetylase 11 (HDAC11), an enzyme that cleaves acyl groups from acylated lysine residues, is the sole member of class IV of HDAC family with no reported crystal structure so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms which complicates the conventional template-based homology modeling. AlphaFold is a neural network machine learning approach for predicting the 3D structures of proteins with atomic accuracy even in absence of similar structures. However, the structures predicted by AlphaFold are missing small molecules as ligands and cofactors. In our study, we first optimized the HDAC11 AlphaFold model by adding the catalytic zinc ion followed by assessment of the usability of the model by docking of the selective inhibitor FT895. Minimization of the optimized model in presence of transplanted inhibitors, which have been described as HDAC11 inhibitors, was performed. Four complexes were generated and proved to be stable using three replicas of 50 ns MD simulations and were successfully utilized for docking of the selective inhibitors FT895, MIR002 and SIS17. For SIS17, The most reasonable pose was selected based on structural comparison between HDAC6, HDAC8 and the HDAC11 optimized AlphaFold model. The manually optimized HDAC11 model is thus able to explain the binding behavior of known HDAC11 inhibitors and can be used for further structure-based optimization.
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Affiliation(s)
- Fady Baselious
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
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75
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Faisal S, Badshah SL, Sharaf M, Abdalla M. Insight into the Hantaan virus RNA-dependent RNA polymerase inhibition using in-silico approaches. Mol Divers 2023; 27:2505-2522. [PMID: 36376718 PMCID: PMC9663193 DOI: 10.1007/s11030-022-10567-6] [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: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
The Hantaan virus (HTN) is a member of the hantaviridae family. It is a segmented type, negative-strand virus (sNSVs). It causes hemorrhagic fever with renal syndrome, which includes fever, vascular hemorrhage, and renal failure. This illness is one of the most serious hemorrhagic diseases in the world, and it is a major public health concern due to its high mortality rate. The Hantaan virus RNA-dependent RNA polymerase complex (RdRp) is involved in viral RNA transcription and replication for the survival and transmission of this virus. Therefore, it is a primary target for antiviral drug development. Interference with the endonucleolytic "cap-snatching" reaction by the HTN virus RdRp endonuclease domain is a particularly appealing approach for drug discovery against this virus. This RdRp endonuclease domain of the HTN virus has a metal-dependent catalytic activity. We targeted this metal-dependent enzymatic activity to identify inhibitors that can bind and disrupt this endonuclease enzyme activity using in-silico approaches i.e., molecular docking, molecular dynamics simulation, predicted absorption, distribution, metabolism, excretion, toxicity (ADMET) and drug-likeness studies. The docking studies showed that peramivir, and ingavirin compounds can effectively bind with the manganese ions and engage with other active site residues of this protein. Molecular simulations also showed stable binding of these ligands with the active site of HTN RdRp. Simulation analysis showed that they were in constant contact with the active site manganese ions and amino acid residues of the HTN virus endonuclease domain. This study will help in better understanding the HTN and related viruses.
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Affiliation(s)
- Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, 25120, Pakistan.
| | - Mohamed Sharaf
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo, 11751, Egypt
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, People's Republic of China
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, 250022, China.
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76
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Wan S, Bhati AP, Coveney PV. Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions. J Chem Theory Comput 2023; 19:7846-7860. [PMID: 37862058 PMCID: PMC10653111 DOI: 10.1021/acs.jctc.3c00842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Indexed: 10/21/2023]
Abstract
Alchemical relative binding free energy calculations have recently found important applications in drug optimization. A series of congeneric compounds are generated from a preidentified lead compound, and their relative binding affinities to a protein are assessed in order to optimize candidate drugs. While methods based on equilibrium thermodynamics have been extensively studied, an approach based on nonequilibrium methods has recently been reported together with claims of its superiority. However, these claims pay insufficient attention to the basis and reliability of both methods. Here we report a comparative study of the two approaches across a large data set, comprising more than 500 ligand transformations spanning in excess of 300 ligands binding to a set of 14 diverse protein targets. Ensemble methods are essential to quantify the uncertainty in these calculations, not only for the reasons already established in the equilibrium approach but also to ensure that the nonequilibrium calculations reside within their domain of validity. If and only if ensemble methods are applied, we find that the nonequilibrium method can achieve accuracy and precision comparable to those of the equilibrium approach. Compared to the equilibrium method, the nonequilibrium approach can reduce computational costs but introduces higher computational complexity and longer wall clock times. There are, however, cases where the standard length of a nonequilibrium transition is not sufficient, necessitating a complete rerun of the entire set of transitions. This significantly increases the computational cost and proves to be highly inconvenient during large-scale applications. Our findings provide a key set of recommendations that should be adopted for the reliable implementation of nonequilibrium approaches to relative binding free energy calculations in ligand-protein systems.
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Affiliation(s)
- Shunzhou Wan
- Centre
for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, U.K.
| | - Agastya P. Bhati
- Centre
for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, U.K.
| | - Peter V. Coveney
- Centre
for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, U.K.
- Advanced
Research Computing Centre, University College
London, London WC1H 0AJ, U.K.
- Computational
Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Amsterdam 1012 WP, Netherlands
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77
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Dai R, Gao H, Su R. Computer-aided drug design for virtual-screening and active-predicting of main protease (M pro) inhibitors against SARS-CoV-2. Front Pharmacol 2023; 14:1288363. [PMID: 38026989 PMCID: PMC10661973 DOI: 10.3389/fphar.2023.1288363] [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: 09/04/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: SARS-CoV-2 is a novel coronavirus with highly contagious and has posed a significant threat to global public health. The main protease (Mpro) is a promising target for antiviral drugs against SARS-CoV-2. Methods: In this study, we have used pharmacophore-based drug design technology to identify potential compounds from drug databases as Mpro inhibitors. Results: The procedure involves pharmacophore modeling, validation, and pharmacophore-based virtual screening, which identifies 257 compounds with promising inhibitory activity. Discussion: Molecular docking and non-bonding interactions between the targeted protein Mpro and compounds showed that ENA482732 was the best compound. These results provided a theoretical foundation for future studies of Mpro inhibitors against SARS-CoV-2.
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Affiliation(s)
| | - Hongwei Gao
- School of Life Science, Ludong University, Yantai, Shandong, China
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78
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Iqbal D, Alsaweed M, Jamal QMS, Asad MR, Rizvi SMD, Rizvi MR, Albadrani HM, Hamed M, Jahan S, Alyenbaawi H. Pharmacophore-Based Screening, Molecular Docking, and Dynamic Simulation of Fungal Metabolites as Inhibitors of Multi-Targets in Neurodegenerative Disorders. Biomolecules 2023; 13:1613. [PMID: 38002295 PMCID: PMC10669353 DOI: 10.3390/biom13111613] [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: 09/21/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Neurodegenerative disorders, such as Alzheimer's disease (AD), negatively affect the economic and psychological system. For AD, there is still a lack of disease-altering treatments and promising cures due to its complex pathophysiology. In this study, we computationally screened the natural database of fungal metabolites against three known therapeutic target proteins of AD. Initially, a pharmacophore-based, drug-likeness category was employed for screening, and it filtered the 14 (A-N) best hits out of 17,544 fungal metabolites. The 14 best hits were docked individually against GSK-3β, the NMDA receptor, and BACE-1 to investigate the potential of finding a multitarget inhibitor. We found that compounds B, F, and L were immuno-toxic, whereas E, H, I, and J had a higher LD50 dose (5000 mg/kg). Among the examined metabolites, the Bisacremine-C (compound I) was found to be the most active molecule against GSK-3β (ΔG: -8.7 ± 0.2 Kcal/mol, Ki: 2.4 × 106 M-1), NMDA (ΔG: -9.5 ± 0.1 Kcal/mol, Ki: 9.2 × 106 M-1), and BACE-1 (ΔG: -9.1 ± 0.2 Kcal/mol, Ki: 4.7 × 106 M-1). It showed a 25-fold higher affinity with GSK-3β, 6.3-fold higher affinity with NMDA, and 9.04-fold higher affinity with BACE-1 than their native ligands, respectively. Molecular dynamic simulation parameters, such as RMSD, RMSF, Rg, and SASA, all confirmed that the overall structures of the targeted enzymes did not change significantly after binding with Bisacremine-C, and the ligand remained inside the binding cavity in a stable conformation for most of the simulation time. The most significant hydrophobic contacts for the GSK-3β-Bisacremine-C complex are with ILE62, VAL70, ALA83, and LEU188, whereas GLN185 is significant for H-bonds. In terms of hydrophobic contacts, TYR184 and PHE246 are the most important, while SER180 is vital for H-bonds in NMDA-Bisacremine-C. THR232 is the most crucial for H-bonds in BACE-1-Bisacremine-C and ILE110-produced hydrophobic contacts. This study laid a foundation for further experimental validation and clinical trials regarding the biopotency of Bisacremine-C.
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Affiliation(s)
- Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia;
| | - Mohammad Rehan Asad
- Department of Basic Medical Science, College of Medicine, Majmaah University, Al Majmaah 11952, Saudi Arabia;
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia;
| | - Moattar Raza Rizvi
- School of Allied Health Sciences, Manav Rachna International Institute of Research & Studies (MRIIRS), Faridabad 121001, India;
| | - Hind Muteb Albadrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia;
| | - Munerah Hamed
- Department of Pathology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Sadaf Jahan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
| | - Hadeel Alyenbaawi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia; (M.A.); (S.J.)
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79
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Wang S, Wang L, Li F, Bai F. DeepSA: a deep-learning driven predictor of compound synthesis accessibility. J Cheminform 2023; 15:103. [PMID: 37919805 PMCID: PMC10621138 DOI: 10.1186/s13321-023-00771-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023] Open
Abstract
With the continuous development of artificial intelligence technology, more and more computational models for generating new molecules are being developed. However, we are often confronted with the question of whether these compounds are easy or difficult to synthesize, which refers to synthetic accessibility of compounds. In this study, a deep learning based computational model called DeepSA, was proposed to predict the synthesis accessibility of compounds, which provides a useful tool to choose molecules. DeepSA is a chemical language model that was developed by training on a dataset of 3,593,053 molecules using various natural language processing (NLP) algorithms, offering advantages over state-of-the-art methods and having a much higher area under the receiver operating characteristic curve (AUROC), i.e., 89.6%, in discriminating those molecules that are difficult to synthesize. This helps users select less expensive molecules for synthesis, reducing the time and cost required for drug discovery and development. Interestingly, a comparison of DeepSA with a Graph Attention-based method shows that using SMILES alone can also efficiently visualize and extract compound's informative features. DeepSA is available online on the below web server ( https://bailab.siais.shanghaitech.edu.cn/services/deepsa/ ) of our group, and the code is available at https://github.com/Shihang-Wang-58/DeepSA .
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Affiliation(s)
- Shihang Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Fenglei Li
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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80
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Hou Y, Bai Y, Lu C, Wang Q, Wang Z, Gao J, Xu H. Applying molecular docking to pesticides. PEST MANAGEMENT SCIENCE 2023; 79:4140-4152. [PMID: 37547967 DOI: 10.1002/ps.7700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
Pesticide creation is related to the development of sustainable agricultural and ecological safety, and molecular docking technology can effectively help in pesticide innovation. This paper introduces the basic theory behind molecular docking, pesticide databases, and docking software. It also summarizes the application of molecular docking in the pesticide field, including the virtual screening of lead compounds, detection of pesticides and their metabolites in the environment, reverse screening of pesticide targets, and the study of resistance mechanisms. Finally, problems with the use of molecular docking technology in pesticide creation are discussed, and prospects for the future use of molecular docking technology in new pesticide development are discussed. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yang Hou
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Yuqian Bai
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Chang Lu
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Qiuchan Wang
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Zishi Wang
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Jinsheng Gao
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Hongliang Xu
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
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81
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Shaikh S, Ali S, Lim JH, Ahmad K, Han KS, Lee EJ, Choi I. Virtual Insights into Natural Compounds as Potential 5α-Reductase Type II Inhibitors: A Structure-Based Screening and Molecular Dynamics Simulation Study. Life (Basel) 2023; 13:2152. [PMID: 38004292 PMCID: PMC10671996 DOI: 10.3390/life13112152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Androgenic alopecia (AGA) is a dermatological disease with psychosocial consequences for those who experience hair loss. AGA is linked to an increase in androgen levels caused by an excess of dihydrotestosterone in blood capillaries produced from testosterone by 5α-reductase type II (5αR2), which is expressed in scalp hair follicles; 5αR2 activity and dihydrotestosterone levels are elevated in balding scalps. The diverse health benefits of flavonoids have been widely reported in epidemiological studies, and research interest continues to increase. In this study, a virtual screening approach was used to identify compounds that interact with active site residues of 5αR2 by screening a library containing 241 flavonoid compounds. Here, we report two potent flavonoid compounds, eriocitrin and silymarin, that interacted strongly with 5αR2, with binding energies of -12.1 and -11.7 kcal/mol, respectively, which were more significant than those of the control, finasteride (-11.2 kcal/mol). Molecular dynamic simulations (200 ns) were used to optimize the interactions between compounds and 5αR2 and revealed that the interaction of eriocitrin and silymarin with 5αR2 was stable. The study shows that eriocitrin and silymarin provide developmental bases for novel 5αR2 inhibitors for the management of AGA.
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Affiliation(s)
- Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Ki Soo Han
- Neo Cremar Co., Ltd., Seoul 05702, Republic of Korea;
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (S.S.); (S.A.); (J.H.L.); (K.A.); (E.J.L.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
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82
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Gautam P, Bisht P, Gautam A, Gupta GD, Singh R, Verma SK. A comprehension on structure guided alignment dependent 3D-QSAR modelling, and molecular dynamics simulation on 2,4-thiazolidinediones as aldose reductase inhibitors for the management of diabetic complications. J Biomol Struct Dyn 2023:1-20. [PMID: 37904329 DOI: 10.1080/07391102.2023.2275190] [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: 06/27/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023]
Abstract
Aldose reductase is an oxo-reductase enzyme belonging to the aldo-keto reductase class. Compounds having thiazolidine-2,4-dione scaffold are reported as potential aldose reductase inhibitors for diabetic complications. The present work uses structure-guided alignment-dependent Gaussian field- and atom-based 3D-QSAR on a dataset of 84 molecules. 3D-QSAR studies on two sets of dataset alignment have been carried out to understand the favourable and unfavourable structural features influencing the affinity of these inhibitors towards the enzyme. Using common pharmacophore hypotheses, the five-point pharmacophores for aldose reductase favourable features were generated. The molecular dynamics simulations (up to 100 ns) were performed for the potent molecule from each alignment set (compounds 24 and 65) compared to reference standard tolrestat and epalrestat to study target-ligand complexes' binding energy and stability. Compound 65 was most stable with better interactions in the aldose reductase binding pocket than tolrestat. The MM-PBSA study suggests compound 65 possessed better binding energy than reference standard tolrestat, i.e. -87.437 ± 19.728 and -73.424 ± 12.502 kJ/mol, respectively. The generated 3D-QSAR models provide information about structure-activity relationships and ligand-target binding energy. Target-specific stability data from MD simulation would be helpful for rational compound design with better aldose reductase activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyadarshi Gautam
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Priya Bisht
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
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83
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Khan M, Kandwal S, Fayne D. DataPype: A Fully Automated Unified Software Platform for Computer-Aided Drug Design. ACS OMEGA 2023; 8:39468-39480. [PMID: 37901539 PMCID: PMC10601415 DOI: 10.1021/acsomega.3c05207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023]
Abstract
With the advent of computer-aided drug design (CADD), traditional physical testing of thousands of molecules has now been replaced by target-focused drug discovery, where potentially bioactive molecules are predicted by computer software before their physical synthesis. However, despite being a significant breakthrough, CADD still faces various limitations and challenges. The increasing availability of data on small molecules has created a need to streamline the sourcing of data from different databases and automate the processing and cleaning of data into a form that can be used by multiple CADD software applications. Several standalone software packages are available to aid the drug designer, each with its own specific application, requiring specialized knowledge and expertise for optimal use. These applications require their own input and output files, making it a challenge for nonexpert users or multidisciplinary discovery teams. Here, we have developed a new software platform called DataPype, which wraps around these different software packages. It provides a unified automated workflow to search for hit compounds using specialist software. Additionally, multiple virtual screening packages can be used in the one workflow, and if different ways of looking at potential hit compounds all predict the same set of molecules, we have higher confidence that we should make or purchase and test the molecules. Importantly, DataPype can run on computer servers, speeding up the virtual screening for new compounds. Combining access to multiple CADD tools within one interface will enhance the early stage of drug discovery, increase usability, and enable the use of parallel computing.
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Affiliation(s)
- Mohemmed
Faraz Khan
- Molecular
Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Integral University, Lucknow U.P., 226026, India
| | - Shubhangi Kandwal
- Molecular
Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Darren Fayne
- Molecular
Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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84
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Bhatt R, Koes DR, Durrant JD. CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.562959. [PMID: 37904961 PMCID: PMC10614872 DOI: 10.1101/2023.10.18.562959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
We present a novel and interpretable approach for predicting small-molecule binding affinities using context explanation networks (CENs). Given the specific structure of a protein/ligand complex, our CENsible scoring function uses a deep convolutional neural network to predict the contributions of pre-calculated terms to the overall binding affinity. We show that CENsible can effectively distinguish active vs. inactive compounds for many systems. Its primary benefit over related machine-learning scoring functions, however, is that it retains interpretability, allowing researchers to identify the contribution of each pre-calculated term to the final affinity prediction, with implications for subsequent lead optimization.
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Affiliation(s)
- Roshni Bhatt
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - David Ryan Koes
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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85
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Cheng J, Yin X, Wang L, Liu X, Yang F, Zhang L, Liu T. Decoding molecular mechanism of species-selective targeting of fungal versus human HSP90 using multiple replica molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2023:1-11. [PMID: 37850420 DOI: 10.1080/07391102.2023.2270687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
As a highly evolutionarily conserved molecular chaperone, heat shock protein (HSP90), plays an important role in virulence traits, representing a therapeutic target for the treatment of fungal infections. The close evolutionary relationship between fungi and their human hosts poses a key challenge for the development of selective antifungal agents. In this work, molecular docking, multiple replica microsecond-based molecular dynamics (MD) simulations, and binding free energy calculations were performed to decode molecular mechanism of species-selective targeting of fungal versus human HSP90 triggered by the compound A11. MD simulations reveal that binding of compound A11 to human HSP90 nucleotide-binding domain (NBD) leads to obvious conformational changes relative to fungal HSP90 NBD. Binding free energy calculations show that the binding of compound A11 to fungal HSP90 NBD is stronger than that to human HSP90 NBD. Per residue-based free energy decomposition analysis was used to evaluate the inhibitor - residue interaction profile. The results efficiently identify the hot spot residues that play vital roles in favorable binding of compound A11 to fungal HSP90 NBD. This study is expected to provide a useful guidance for the development of selective inhibitors toward fungal HSP90.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jinying Cheng
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Xue Yin
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Lulu Wang
- Department of Critical Care Medicine, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Xianxian Liu
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Fang Yang
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Liguo Zhang
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Tonggang Liu
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
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86
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Zhang C, Sui Y, Liu S, Yang M. Anti-Viral Activity of Bioactive Molecules of Silymarin against COVID-19 via In Silico Studies. Pharmaceuticals (Basel) 2023; 16:1479. [PMID: 37895950 PMCID: PMC10610370 DOI: 10.3390/ph16101479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection drove the global coronavirus disease 2019 (COVID-19) pandemic, causing a huge loss of human life and a negative impact on economic development. It is an urgent necessity to explore potential drugs against viruses, such as SARS-CoV-2. Silymarin, a mixture of herb-derived polyphenolic flavonoids extracted from the milk thistle, possesses potent antioxidative, anti-apoptotic, and anti-inflammatory properties. Accumulating research studies have demonstrated the killing activity of silymarin against viruses, such as dengue virus, chikungunya virus, and hepatitis C virus. However, the anti-COVID-19 mechanisms of silymarin remain unclear. In this study, multiple disciplinary approaches and methodologies were applied to evaluate the potential mechanisms of silymarin as an anti-viral agent against SARS-CoV-2 infection. In silico approaches such as molecular docking, network pharmacology, and bioinformatic methods were incorporated to assess the ligand-protein binding properties and analyze the protein-protein interaction network. The DAVID database was used to analyze gene functions, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment. TCMSP and GeneCards were used to identify drug target genes and COVID-19-related genes. Our results revealed that silymarin compounds, such as silybin A/B and silymonin, displayed triplicate functions against SARS-CoV-2 infection, including directly binding with human angiotensin-converting enzyme 2 (ACE2) to inhibit SARS-CoV-2 entry into the host cells, directly binding with viral proteins RdRp and helicase to inhibit viral replication and proliferation, and regulating host immune response to indirectly inhibit viral infection. Specifically, the targets of silymarin molecules in immune regulation were screened out, such as proinflammatory cytokines TNF and IL-6 and cell growth factors VEGFA and EGF. In addition, the molecular mechanism of drug-target protein interaction was investigated, including the binding pockets of drug molecules in human ACE2 and viral proteins, the formation of hydrogen bonds, hydrophobic interactions, and other drug-protein ligand interactions. Finally, the drug-likeness results of candidate molecules passed the criteria for drug screening. Overall, this study demonstrates the molecular mechanism of silymarin molecules against SARS-CoV-2 infection.
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Affiliation(s)
- Chunye Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA;
| | - Yuxiang Sui
- School of Life Science, Shanxi Normal University, Linfen 041004, China;
| | - Shuai Liu
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310006, China;
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO 65212, USA
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA
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87
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Muthusamy K, Ramasamy G, Ravikumar C, Natesan S, Muthurajan R, Uthandi S, Kalyanasundaram K, Tiwari V. Exploring bixin from Bixa orellana L. seeds: quantification and in silico insights into its anti-cancer potential. J Biomol Struct Dyn 2023:1-15. [PMID: 37837422 DOI: 10.1080/07391102.2023.2268202] [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: 03/29/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Bixin, the key pigment of Bixa orellana L., is an apo-carotenoid found in the seed arils. The present study aimed to quantitatively determine the bixin content of seeds and explore its anti-cancer activity through in silico studies. The bixin content from the seeds of the local genotype, TNMTP8, quantified by RP-HPLC was 4.58 mg per gram. The prediction of pharmacological activity suggested that bixin may serve as a BRAF, MMP9, TNF expression inhibitors, and TP53 expression enhancer. According to molecular docking analysis, bixin interacted with eight different skin cancer targets and had the lowest binding energy compared to the standard drug, 5-fluorouracil. The binding score between bixin and the targets ranged from -4.7 to -8.7 kcal/mol. The targets BRAF and SIRT3 interacted well with bixin, with binding energies as low as -8.3 and -8.7 kcal/mol, respectively. Hence, the dynamic behavior of these two docked complexes throughout a 500 ns trajectory run was investigated further. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) values, and total contacts as a function of time recorded during scrutiny suggest that both complexes were stable. This was validated by post-molecular dynamics analysis using Molecular Mechanics Generalized Born Surface Area (MM-GBSA). Principal component analysis (PCA) was used to analyze the significant differences in motion exhibited by BRAF-Bixin and SIRT3-Bixin. The results showed that bixin is a promising source for potential treatment interventions in skin cancer therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kaviyapriya Muthusamy
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Gnanam Ramasamy
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Caroline Ravikumar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Senthil Natesan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Sivakumar Uthandi
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Kumaran Kalyanasundaram
- Department of Forest Biology and Tree Improvement, Forest College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
| | - Vikas Tiwari
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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88
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Lundborg M, Lidmar J, Hess B. On the Path to Optimal Alchemistry. Protein J 2023; 42:477-489. [PMID: 37651042 PMCID: PMC10480267 DOI: 10.1007/s10930-023-10137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 09/01/2023]
Abstract
Alchemical free energy calculations have become a standard and widely used tool, in particular for calculating and comparing binding affinities of drugs. Although methods to compute such free energies have improved significantly over the last decades, the choice of path between the end states of interest is usually still the same as two decades ago. We will show that there is a fundamentally arbitrary, implicit choice of parametrization of this path. To address this, the notion of the length of a path or a metric is required. A metric recently introduced in the context of the accelerated weight histogram method also proves to be very useful here. We demonstrate that this metric can not only improve the efficiency of sampling along a given path, but that it can also be used to improve the actual choice of path. For a set of relevant use cases, the combination of these improvements can increase the efficiency of alchemical free energy calculations by up to a factor 16.
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Affiliation(s)
| | - Jack Lidmar
- Department of Physics, KTH Royal Institute of Technology, 10691, Stockholm, Sweden
| | - Berk Hess
- Department of Applied Physics, KTH Royal Institute of Technology, 10691, Stockholm, Science for Life Laboratory, Solna, Sweden.
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89
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Gómez-García A, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, Bolzani VDS, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Valencia Sánchez HA, Cortés Hernández HF, Medina-Franco JL. Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals (Basel) 2023; 16:1388. [PMID: 37895859 PMCID: PMC10609821 DOI: 10.3390/ph16101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.
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Affiliation(s)
- Alejandro Gómez-García
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
| | - Daniel A. Acuña Jiménez
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
| | - William J. Zamora
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José 1174-1200, Costa Rica
| | - Haruna L. Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Miguel Á. Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Adriano D. Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Vanderlan da S. Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, Araraquara 14800-900, SP, Brazil;
| | - Dionisio A. Olmedo
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Pablo N. Solís
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Marvin J. Núñez
- Natural Product Research Laboratory, School of Chemistry and Pharmacy, University of El Salvador, Final Ave. Mártires Estudiantes del 30 de Julio, San Salvador 01101, El Salvador;
| | - Johny R. Rodríguez Pérez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
- GIEPRONAL Research Group, School of Basic Sciences, Technology and Engineering, Universidad Nacional Abierta y a Distancia, Dosquebradas 661001, Colombia
| | - Hoover A. Valencia Sánchez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - Héctor F. Cortés Hernández
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
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90
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Li J, Kumar A, Långström B, Nordberg A, Ågren H. Insight into the Binding of First- and Second-Generation PET Tracers to 4R and 3R/4R Tau Protofibrils. ACS Chem Neurosci 2023; 14:3528-3539. [PMID: 37639522 PMCID: PMC10515481 DOI: 10.1021/acschemneuro.3c00437] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Primary supranuclear palsy (PSP) is a rare neurodegenerative disease that perturbs body movement, eye movement, and walking balance. Similar to Alzheimer's disease (AD), the abnormal aggregation of tau fibrils in the central neuronal and glial cells is a major hallmark of PSP disease. In this study, we use multiple approaches, including docking, molecular dynamics, and metadynamics simulations, to investigate the binding mechanism of 10 first- and second-generations of PET tracers for PSP tau and compare their binding in cortical basal degeneration (CBD) and AD tauopathies. Structure-activity relationships, binding preferences, the nature of ligand binding in terms of basic intermolecular interactions, the role of polar/charged residues, induced-fit mechanisms, grove closures, and folding patterns for the binding of these tracers in PSP, CBD, and AD tau fibrils are evaluated and discussed in detail in order to build a holistic picture of what is essential for the binding and also to rank the potency of the different tracers. For example, we found that the same tracer shows different binding preferences for the surface sites of tau fibrils that are intrinsically distinct in the folding patterns. Results from the metadynamics simulations predict that PMPBB3 and PBB3 exhibit the strongest binding free energies onto the Q276[I277]I278, Q351[S352]K353, and N368[K369]K370 sites of PSP than the other explored tracers, indicating a solid preference for vdW and cation-π interactions. Our results also reproduced known preferences of tracers, namely, that MK6240 binds better to AD tau than CBD tau and PSP tau and that CBD2115, PI2620, and PMPBB3 are 4R tau binders. These findings fill in the well-sought-after knowledge gap in terms of these tracers' potential binding mechanisms and will be important for the design of highly selective novel PET tracers for tauopathies.
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Affiliation(s)
- Junhao Li
- Department
of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Amit Kumar
- Department
of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, Center for Alzheimer Research, Neo, 141 84 Stockholm, Sweden
| | - Bengt Långström
- Department
of Chemistry - BMC, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Agneta Nordberg
- Department
of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, Center for Alzheimer Research, Neo, 141 84 Stockholm, Sweden
- Theme
Inflammation and Aging, Karolinska University
Hospital, S-141 86 Stockholm, Sweden
| | - Hans Ågren
- Department
of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- College
of Chemistry and Chemical Engineering, Henan
University, Kaifeng, Henan 475004, P. R. China
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91
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Gao J, Shen Z, Xie Y, Lu J, Lu Y, Chen S, Bian Q, Guo Y, Shen L, Wu J, Zhou B, Hou T, He Q, Che J, Dong X. TransFoxMol: predicting molecular property with focused attention. Brief Bioinform 2023; 24:bbad306. [PMID: 37605947 DOI: 10.1093/bib/bbad306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
Predicting the biological properties of molecules is crucial in computer-aided drug development, yet it's often impeded by data scarcity and imbalance in many practical applications. Existing approaches are based on self-supervised learning or 3D data and using an increasing number of parameters to improve performance. These approaches may not take full advantage of established chemical knowledge and could inadvertently introduce noise into the respective model. In this study, we introduce a more elegant transformer-based framework with focused attention for molecular representation (TransFoxMol) to improve the understanding of artificial intelligence (AI) of molecular structure property relationships. TransFoxMol incorporates a multi-scale 2D molecular environment into a graph neural network + Transformer module and uses prior chemical maps to obtain a more focused attention landscape compared to that obtained using existing approaches. Experimental results show that TransFoxMol achieves state-of-the-art performance on MoleculeNet benchmarks and surpasses the performance of baselines that use self-supervised learning or geometry-enhanced strategies on small-scale datasets. Subsequent analyses indicate that TransFoxMol's predictions are highly interpretable and the clever use of chemical knowledge enables AI to perceive molecules in a simple but rational way, enhancing performance.
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Affiliation(s)
- Jian Gao
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zheyuan Shen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yufeng Xie
- School of Software Technology, Zhejiang University, Hangzhou, China
| | - Jialiang Lu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yang Lu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Sikang Chen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qingyu Bian
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yue Guo
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Liteng Shen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jian Wu
- School of Software Technology, Zhejiang University, Hangzhou, China
| | - Binbin Zhou
- Department of Computer Science and Computing, Zhejiang University City College, Hangzhou, China
| | - Tingjun Hou
- State Key Lab of CAD&CG, College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
- Centre for Drug Safety Evaluation and Research of ZJU, Hangzhou, 310058, PR China
- Cancer Center of Zhejiang University, Hangzhou, China
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
- Cancer Center of Zhejiang University, Hangzhou, China
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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92
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Borba JB, de Azevedo BR, Ferreira LA, Rimoldi A, Salazar Alvarez LC, Calit J, Bargieri DY, Costa FTM, Andrade CH. Transcriptomics-Guided In Silico Drug Repurposing: Identifying New Candidates with Dual-Stage Antiplasmodial Activity. ACS OMEGA 2023; 8:34084-34090. [PMID: 37744849 PMCID: PMC10515587 DOI: 10.1021/acsomega.3c05138] [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: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
In tropical and subtropical areas, malaria stands as a profound public health challenge, causing an estimated 247 million cases worldwide annually. Given the absence of a viable vaccine, the timely and effective treatment of malaria remains a critical priority. However, the growing resistance of parasites to currently utilized drugs underscores the critical need for the identification of new antimalarial therapies. Here, we aimed to identify potential new drug candidates against Plasmodium falciparum, the main causative agent of malaria, by analyzing the transcriptomes of different life stages of the parasite and identifying highly expressed genes. We searched for genes that were expressed in all stages of the parasite's life cycle, including the asexual blood stage, gametocyte stage, liver stage, and sexual stages in the insect vector, using transcriptomics data from publicly available databases. From this analysis, we found 674 overlapping genes, including 409 essential ones. By searching through drug target databases, we discovered 70 potential drug targets and 75 associated bioactive compounds. We sought to expand this analysis to similar compounds to known drugs. So, we found a list of 1557 similar compounds, which we predicted as actives and inactives using previously developed machine learning models against five life stages of Plasmodium spp. From this analysis, two compounds were selected, and the reactions were experimentally evaluated. The compounds HSP-990 and silvestrol aglycone showed potent inhibitory activity at nanomolar concentrations against the P. falciparum 3D7 strain asexual blood stage. Moreover, silvestrol aglycone exhibited low cytotoxicity in mammalian cells, transmission-blocking potential, and inhibitory activity comparable to those of established antimalarials. These findings warrant further investigation of silvestrol aglycone as a potential dual-acting antimalarial and transmission-blocking candidate for malaria control.
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Affiliation(s)
- Joyce
V. B. Borba
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculdade de Farmacia, Universidade Federal de Goias, 74605-170 Goiânia, Goiás, Brazil
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Beatriz Rosa de Azevedo
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculdade de Farmacia, Universidade Federal de Goias, 74605-170 Goiânia, Goiás, Brazil
| | - Larissa A. Ferreira
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Aline Rimoldi
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Luís C. Salazar Alvarez
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Juliana Calit
- Department
of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
| | - Daniel Y. Bargieri
- Department
of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
| | - Fabio T. M. Costa
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Carolina Horta Andrade
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculdade de Farmacia, Universidade Federal de Goias, 74605-170 Goiânia, Goiás, Brazil
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93
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Yasir M, Park J, Han ET, Park WS, Han JH, Kwon YS, Lee HJ, Chun W. Vismodegib Identified as a Novel COX-2 Inhibitor via Deep-Learning-Based Drug Repositioning and Molecular Docking Analysis. ACS OMEGA 2023; 8:34160-34170. [PMID: 37744812 PMCID: PMC10515398 DOI: 10.1021/acsomega.3c05425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Artificial intelligence algorithms have been increasingly applied in drug development due to their efficiency and effectiveness. Deep-learning-based drug repurposing can contribute to the identification of novel therapeutic applications for drugs with other indications. The current study used a trained deep-learning model to screen an FDA-approved drug library for novel COX-2 inhibitors. Reference COX-2 data sets, composed of active and decoy compounds, were obtained from the DUD-E database. To extract molecular features, compounds were subjected to RDKit, a cheminformatic toolkit. GraphConvMol, a graph convolutional network model from DeepChem, was applied to obtain a predictive model from the DUD-E data sets. Then, the COX-2 inhibitory potential of the FDA-approved drugs was predicted using the trained deep-learning model. Vismodegib, an anticancer agent that inhibits the hedgehog signaling pathway by binding to smoothened, was predicted to inhibit COX-2. Noticeably, some compounds that exhibit high potential from the prediction were known to be COX-2 inhibitors, indicating the prediction model's liability. To confirm the COX-2 inhibition activity of vismodegib, molecular docking was carried out with the reference compounds of the COX-2 inhibitor, celecoxib, and ibuprofen. Furthermore, the experimental examination of COX-2 inhibition was also carried out using a cell culture study. Results showed that vismodegib exhibited a highly comparable COX-2 inhibitory activity compared to celecoxib and ibuprofen. In conclusion, the deep-learning model can efficiently improve the virtual screening of drugs, and vismodegib can be used as a novel COX-2 inhibitor.
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Affiliation(s)
- Muhammad Yasir
- Department
of Pharmacology, Kangwon National University
School of Medicine, Chuncheon24341, Republic
of Korea
| | - Jinyoung Park
- Department
of Pharmacology, Kangwon National University
School of Medicine, Chuncheon24341, Republic
of Korea
| | - Eun-Taek Han
- Department
of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Won Sun Park
- Department
of Physiology, Kangwon National University
School of Medicine, Chuncheon24341, Republic
of Korea
| | - Jin-Hee Han
- Department
of Medical Environmental Biology and Tropical Medicine, Kangwon National University School of Medicine, Chuncheon 24341, Republic of Korea
| | - Yong-Soo Kwon
- College
of Pharmacy, Kangwon National University
School of Medicine, Chuncheon24341, Republic
of Korea
| | - Hee-Jae Lee
- Department
of Pharmacology, Kangwon National University
School of Medicine, Chuncheon24341, Republic
of Korea
| | - Wanjoo Chun
- Department
of Pharmacology, Kangwon National University
School of Medicine, Chuncheon24341, Republic
of Korea
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94
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Menendez CA, Mohamed A, Perez-Lemus GR, Weiss AM, Rawe BW, Liu G, Crolais AE, Kenna E, Byléhn F, Alvarado W, Mendels D, Rowan SJ, Tay S, de Pablo JJ. Development of Masitinib Derivatives with Enhanced M pro Ligand Efficiency and Reduced Cytotoxicity. Molecules 2023; 28:6643. [PMID: 37764425 PMCID: PMC10536273 DOI: 10.3390/molecules28186643] [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: 08/02/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Recently, a high-throughput screen of 1900 clinically used drugs identified masitinib, an orally bioavailable tyrosine kinase inhibitor, as a potential treatment for COVID-19. Masitinib acts as a broad-spectrum inhibitor for human coronaviruses, including SARS-CoV-2 and several of its variants. In this work, we rely on atomistic molecular dynamics simulations with advanced sampling methods to develop a deeper understanding of masitinib's mechanism of Mpro inhibition. To improve the inhibitory efficiency and to increase the ligand selectivity for the viral target, we determined the minimal portion of the molecule (fragment) that is responsible for most of the interactions that arise within the masitinib-Mpro complex. We found that masitinib forms highly stable and specific H-bond interactions with Mpro through its pyridine and aminothiazole rings. Importantly, the interaction with His163 is a key anchoring point of the inhibitor, and its perturbation leads to ligand unbinding within nanoseconds. Based on these observations, a small library of rationally designed masitinib derivatives (M1-M5) was proposed. Our results show increased inhibitory efficiency and highly reduced cytotoxicity for the M3 and M4 derivatives compared to masitinib.
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Affiliation(s)
- Cintia A. Menendez
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Adil Mohamed
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Gustavo R. Perez-Lemus
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Adam M. Weiss
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Benjamin W. Rawe
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Guancen Liu
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Alex E. Crolais
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Emma Kenna
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Fabian Byléhn
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Walter Alvarado
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Dan Mendels
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Stuart J. Rowan
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
- Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
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95
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Alom MM, Bonna RP, Islam A, Alom MW, Rahman ME, Faruqe MO, Khalekuzzaman M, Zaman R, Islam MA. Unveiling Neuroprotective Potential of Spice Plant-Derived Compounds against Alzheimer's Disease: Insights from Computational Studies. Int J Alzheimers Dis 2023; 2023:8877757. [PMID: 37744007 PMCID: PMC10516701 DOI: 10.1155/2023/8877757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/26/2023] [Accepted: 08/26/2023] [Indexed: 09/26/2023] Open
Abstract
Alzheimer's disease (AD) is a serious threat to the global health care system and is brought on by a series of factors that cause neuronal dysfunction and impairment in memory and cognitive decline. This study investigated the therapeutic potential of phytochemicals that belong to the ten regularly used spice plants, based on their binding affinity with AD-associated proteins. Comprehensive docking studies were performed using AutoDock Vina in PyRx followed by molecular dynamic (MD) simulations using AMBER 14. The docking study of the chosen molecules revealed the binding energies of their interactions with the target proteins, while MD simulations were carried out to verify the steadiness of bound complexes. Through the Lipinski filter and admetSAR analysis, the chosen compounds' pharmacokinetic characteristics and drug likeness were also examined. The pharmacophore mapping study was also done and analyzed for best selected molecules. Additionally, principal component analysis (PCA) was used to examine how the general motion of the protein changed. The results showed quercetin and myricetin to be potential inhibitors of AChE and alpha-amyrin and beta-chlorogenin to be potential inhibitors of BuChE, exhibiting best binding energies comparable to those of donepezil, used as a positive control. The multiple descriptors from the simulation study, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bond, radius of gyration (Rg), and solvent-accessible surface areas (SASA), confirm the stable nature of the protein-ligand complexes. Molecular mechanic Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations indicated the energetically favorable binding of the ligands to the protein. Finally, according to pharmacokinetic properties and drug likeness, characteristics showed that quercetin and myricetin for AChE and alpha-amyrin and beta-chlorogenin for BuChE were found to be the most effective agents for treating the AD.
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Affiliation(s)
- Md. Murshid Alom
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Rejwana Parvin Bonna
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Ariful Islam
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Wasim Alom
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Ekhtiar Rahman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Khalekuzzaman
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Rashed Zaman
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Asadul Islam
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
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96
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Pakotiprapha D, Kuhaudomlarp S, Tinikul R, Chanarat S. Bridging the Gap: Can COVID-19 Research Help Combat African Swine Fever? Viruses 2023; 15:1925. [PMID: 37766331 PMCID: PMC10536364 DOI: 10.3390/v15091925] [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: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
African swine fever (ASF) is a highly contagious and economically devastating disease affecting domestic pigs and wild boar, caused by African swine fever virus (ASFV). Despite being harmless to humans, ASF poses significant challenges to the swine industry, due to sudden losses and trade restrictions. The ongoing COVID-19 pandemic has spurred an unparalleled global research effort, yielding remarkable advancements across scientific disciplines. In this review, we explore the potential technological spillover from COVID-19 research into ASF. Specifically, we assess the applicability of the diagnostic tools, vaccine development strategies, and biosecurity measures developed for COVID-19 for combating ASF. Additionally, we discuss the lessons learned from the pandemic in terms of surveillance systems and their implications for managing ASF. By bridging the gap between COVID-19 and ASF research, we highlight the potential for interdisciplinary collaboration and technological spillovers in the battle against ASF.
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Affiliation(s)
| | | | | | - Sittinan Chanarat
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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97
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Li L, Liu S, Wang B, Liu F, Xu S, Li P, Chen Y. An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design Approaches. Int J Mol Sci 2023; 24:13953. [PMID: 37762253 PMCID: PMC10530957 DOI: 10.3390/ijms241813953] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Small molecule kinase inhibitors (SMKIs) are of heightened interest in the field of drug research and development. There are 79 (as of July 2023) small molecule kinase inhibitors that have been approved by the FDA and hundreds of kinase inhibitor candidates in clinical trials that have shed light on the treatment of some major diseases. As an important strategy in drug design, computer-aided drug design (CADD) plays an indispensable role in the discovery of SMKIs. CADD methods such as docking, molecular dynamic, quantum mechanics/molecular mechanics, pharmacophore, virtual screening, and quantitative structure-activity relationship have been applied to the design and optimization of small molecule kinase inhibitors. In this review, we provide an overview of recent advances in CADD and SMKIs and the application of CADD in the discovery of SMKIs.
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Affiliation(s)
- Linwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Songtao Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Bi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Fei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Shu Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Pirui Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yu Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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98
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Adeoye AO, Porta DJ, Rivoira MA, Garcia NH. Pharmacoinformatics studies of coenzyme Q10 and potassium polyacrylate on angiotensin-converting enzyme associated with hypertension. J Biomol Struct Dyn 2023:1-12. [PMID: 37667993 DOI: 10.1080/07391102.2023.2254395] [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: 05/08/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023]
Abstract
Coenzyme Q10's (CoQ10) favorable impact on cardiovascular diseases risk factors like hypertension and atherosclerosis is linked to the antioxidant action of CoQ10 in these conditions. This study showed the possible effects of CoQ10, potassium polyacrylate (PCK), and valsartan, a reference drug, on the angiotensin-converting enzyme (ACE), a crucial component of the renin-angiotensin system. The Glide tool on Maestro 11.1 was used to calculate the respective binding affinity and binding energy of these compounds towards ACE. The Schrödinger suite was used to run molecular dynamic simulations for 100 ns. The pkCSM tool was used to forecast the pharmacokinetic characteristics and toxicological effects. The SwissADME server was used to estimate the drug-like properties of these compounds. Based on their corresponding scoring values and the negative values of the binding free energies, molecular docking analysis of CoQ10 and PCK revealed that both exhibited favorable binding affinities towards the ACE, with CoQ10 having the highest binding scores. The results showed that both CoQ10 and PCK and the reference drug, valsartan, have some amino acids in common (at the pocket site of ACE) as the key residues for binding to ACE. Both CoQ10 and PCK demonstrated drug-like qualities and were not harmful, according to the predicted pharmacokinetics and toxicology studies. The results of this study suggest that because of its inhibitory interactions with ACE, CoQ10 in particular could be useful in regulating and reducing hypertension.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akinwunmi O Adeoye
- INICSA, Enrique Barros Pabellón Biología Celular, Ciudad Universitaria, Córdoba, Argentina
- Department of Biochemistry, Federal University Oye-Ekiti, Oye, Nigeria
| | - Daniela J Porta
- INICSA, Enrique Barros Pabellón Biología Celular, Ciudad Universitaria, Córdoba, Argentina
| | - María A Rivoira
- INICSA, Enrique Barros Pabellón Biología Celular, Ciudad Universitaria, Córdoba, Argentina
| | - Néstor H Garcia
- INICSA, Enrique Barros Pabellón Biología Celular, Ciudad Universitaria, Córdoba, Argentina
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99
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Chua HM, Moshawih S, Goh HP, Ming LC, Kifli N. Insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment: A protocol for systematic review. PLoS One 2023; 18:e0290948. [PMID: 37656730 PMCID: PMC10473489 DOI: 10.1371/journal.pone.0290948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/20/2023] [Indexed: 09/03/2023] Open
Abstract
There is still unmet medical need in cancer treatment mainly due to drug resistance and adverse drug events. Therefore, the search for better drugs is essential. Computer-aided drug design (CADD) and discovery tools are useful to streamline the lengthy and costly drug development process. Anthraquinones are a group of naturally occurring compounds with unique scaffold that exert various biological properties including anticancer activities. This protocol describes a systematic review that provide insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment. It was prepared in accordance with the "Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 guidelines, and published in the "International prospective register of systematic reviews" database (PROSPERO: CRD42023432904). Search strategies will be developed based on the combination of relevant keywords and executed in PubMed, Scopus, Web of Science and MedRxiv. Only original studies that employed CADD as primary tool in virtual screening for the purpose of designing or discovering anti-cancer drugs involving anthraquinone scaffold published in English language will be included. Two independent reviewers will be involved to screen and select the papers, extract the data and assess the risk of bias. Apart from exploring the trends and types of CADD methods used, the target proteins of these compounds in cancer treatment will also be revealed in this review. It is believed that the outcome of this study could be utilized to support the ongoing research in similar area with better quality and greater probability of success, consequently optimizing the resources in subsequent in vitro, in vivo, non-clinical and clinical development. It will also serve as an evidence based scientific guide for new research to design novel anthraquinone-derived drug with improved efficacy and safety profile for cancer treatment.
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Affiliation(s)
- Hui Ming Chua
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, University Brunei Darussalam, Gadong, Brunei Darussalam
| | - Said Moshawih
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, University Brunei Darussalam, Gadong, Brunei Darussalam
| | - Hui Poh Goh
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, University Brunei Darussalam, Gadong, Brunei Darussalam
| | - Long Chiau Ming
- School of Medical and Lifesciences, Sunway University, Bandar Sunway, Malaysia
| | - Nurolaini Kifli
- PAP Rashidah Sa’adatul Bolkiah Institute of Health Sciences, University Brunei Darussalam, Gadong, Brunei Darussalam
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Alshehri SA, Wahab S, Almoyad MAA. In silico identification of potential protein kinase C alpha inhibitors from phytochemicals from IMPPAT database for anticancer therapeutics: a virtual screening approach. J Biomol Struct Dyn 2023:1-12. [PMID: 37643015 DOI: 10.1080/07391102.2023.2252086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/19/2023] [Indexed: 08/31/2023]
Abstract
Protein Kinase C alpha (PKCα) is a critical signaling molecule that plays a crucial role in various physiological processes, including cell growth, differentiation, and survival. Over the years, there has been a growing interest in targeting PKCα as a promising drug target for the treatment of various diseases, including cancer. Targeting PKCα can, therefore, serve as a potential strategy to prevent cancer progression and enhance the efficacy of conventional anticancer therapies. We conducted a systematic search for promising compounds for their anticancer potential that target PKCα using natural compounds from the IMPPAT database. The initial compounds were screened through various tests, including analysis of their physical and chemical properties, PAINS filter, ADMET analysis, PASS analysis, and specific interaction analysis. We selected those that showed high binding affinity and specificity to PKCα from the screened compounds, and we further analyzed them using molecular dynamics simulations (MDS) and principal component analysis (PCA). Various systematic parameters from the MDS analyses suggested that the protein-ligand complexes were stabilized throughout the simulation trajectories of 100 nanoseconds (ns). Our findings indicated that compounds Nicandrenone and Withaphysalin D bind to PKCα with high stability and affinity, making them potential candidates for further research in cancer therapeutics innovation in clinical contexts.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saad Ali Alshehri
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences in Khamis Mushyt, King Khalid University, Abha, Saudi Arabia
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