51
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Trends and hotspots for European Journal of Medicinal Chemistry: A bibliometric study. Eur J Med Chem 2023; 247:115041. [PMID: 36566715 DOI: 10.1016/j.ejmech.2022.115041] [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: 09/26/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
European Journal of Medicinal Chemistry (EJMC) has been around for a long time and has gained broad interest from the various individuals working in the field. However, there is no bibliometric analysis on the publications of EJMC to thoroughly assess the scientific output and current status systematically. Therefore, the study was conducted to analyze the various publications of EJMC from 1987 to 2022 to improve their quality. A total of 13,386 papers were retrieved, with the number of publications increasing yearly. Based on the multiple indicators of bibliometrics, the highest impact countries, institutions, authors and representative literature were identified, and visualization networks were constructed using VOSviewer. Keyword co-occurrence analysis reveals a gradual shift from phenotypic drug discovery to target-based drug discovery in the EJMC theme change. Moreover, further discussion of the keyword clustering results is provided to support researchers in defining the scope of their research topics and planning their research directions. At this stage, there is a greater focus on developing antitumor and oxidative stress-related drugs than on the earlier anti-infective activities. In future studies, the main research directions are tumor multidrug resistance, oxidative stress, and dual inhibitors.
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52
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Effect of Antihypertensive Drug (Chlorothiazide) on Fibrillation of Lysozyme: A Combined Spectroscopy, Microscopy, and Computational Study. Int J Mol Sci 2023; 24:ijms24043112. [PMID: 36834523 PMCID: PMC9959601 DOI: 10.3390/ijms24043112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Amyloid fibrils abnormally accumulate together in the human body under certain conditions, which can result in lethal conditions. Thus, blocking this aggregation may prevent or treat this disease. Chlorothiazide (CTZ) is a diuretic and is used to treat hypertension. Several previous studies suggest that diuretics prevent amyloid-related diseases and reduce amyloid aggregation. Thus, in this study we examine the effects of CTZ on hen egg white lysozyme (HEWL) aggregation using spectroscopic, docking, and microscopic approaches. Our results showed that under protein misfolding conditions of 55 °C, pH 2.0, and 600 rpm agitation, HEWL aggregated as evidenced by the increased turbidity and Rayleigh light scattering (RLS). Furthermore, thioflavin-T, as well as trans electron microscope (TEM) analysis confirmed the formation of amyloid structures. An anti-aggregation effect of CTZ is observed on HEWL aggregations. Circular dichroism (CD), TEM, and Thioflavin-T fluorescence show that both CTZ concentrations reduce the formation of amyloid fibrils as compared to fibrillated. The turbidity, RLS, and ANS fluorescence increase with CTZ increasing. This increase is attributed to the formation of a soluble aggregation. As evidenced by CD analysis, there was no significant difference in α-helix content and β-sheet content between at 10 µM CTZ and 100 µM. A TEM analysis of HEWL coincubated with CTZ at different concentrations validated all the above-mentioned results. The TEM results show that CTZ induces morphological changes in the typical structure of amyloid fibrils. The steady-state quenching study demonstrated that CTZ and HEWL bind spontaneously via hydrophobic interactions. HEWL-CTZ also interacts dynamically with changes in the environment surrounding tryptophan. Computational results revealed the binding of CTZ to ILE98, GLN57, ASP52, TRP108, TRP63, TRP63, ILE58, and ALA107 residues in HEWL via hydrophobic interactions and hydrogen bonds with a binding energy of -6.58 kcal mol-1. We suggest that at 10 µM and 100 μM, CTZ binds to the aggregation-prone region (APR) of HEWL and stabilizes it, thus preventing aggregation. Based on these findings, we can conclude that CTZ has antiamyloidogenic activity and can prevent fibril aggregation.
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53
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Ejeh S, Uzairu A, Shallangwa GA, Abechi SE, Ibrahim MT, Ramu R, Al-Ghorbani M. Chemical bioinformatics study of Nonadec-7-ene-4-carboxylic acid derivatives via molecular docking, and molecular dynamic simulations to identify novel lead inhibitors of hepatitis c virus NS3/4a protease. SCIENTIFIC AFRICAN 2023. [DOI: 10.1016/j.sciaf.2023.e01591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
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54
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Huang J, Xu Y, Xue Y, Huang Y, Li X, Chen X, Xu Y, Zhang D, Zhang P, Zhao J, Ji J. Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences. Nat Biomed Eng 2023:10.1038/s41551-022-00991-2. [PMID: 36635418 DOI: 10.1038/s41551-022-00991-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/29/2022] [Indexed: 01/14/2023]
Abstract
Systematically identifying functional peptides is difficult owing to the vast combinatorial space of peptide sequences. Here we report a machine-learning pipeline that mines the hundreds of billions of sequences in the entire virtual library of peptides made of 6-9 amino acids to identify potent antimicrobial peptides. The pipeline consists of trainable machine-learning modules (for performing empirical selection, classification, ranking and regression tasks) assembled sequentially following a coarse-to-fine design principle to gradually narrow down the search space. The leading three antimicrobial hexapeptides identified by the pipeline showed strong activities against a wide range of clinical isolates of multidrug-resistant pathogens. In mice with bacterial pneumonia, aerosolized formulations of the identified peptides showed therapeutic efficacy comparable to penicillin, negligible toxicity and a low propensity to induce drug resistance. The machine-learning pipeline may accelerate the discovery of new functional peptides.
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Affiliation(s)
- Junjie Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yanchao Xu
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yunfan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xu Li
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaohui Chen
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Yao Xu
- R&D Department of AtaGenix Laboratories Co., Ltd. (Wuhan), Wuhan, China
| | - Dongxiang Zhang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Peng Zhang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
| | - Junbo Zhao
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China.
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
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55
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Identification of a Novel Dual Inhibitor of Acetylcholinesterase and Butyrylcholinesterase: In Vitro and In Silico Studies. Pharmaceuticals (Basel) 2023; 16:ph16010095. [PMID: 36678592 PMCID: PMC9864454 DOI: 10.3390/ph16010095] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
The enhancement of cholinergic functions via acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibition is considered a valuable therapeutic strategy for the treatment of Alzheimer's disease. This study aimed to evaluate the in vitro effect of ZINC390718, previously filtered using computational approaches, on both cholinesterases and to characterize, using a molecular dynamics (MD) simulation, the possible binding mode of this compound inside the cholinesterase enzymes. The in vitro cytotoxicity effect was also investigated using a primary astrocyte-enriched glial cell culture. ZINC390718 presented in vitro dual inhibitory activity against AChE at a high micromolar range (IC50 = 543.8 µM) and against BuChE (IC50 = 241.1 µM) in a concentration-dependent manner, with greater activity against BuChE. The MD simulation revealed that ZINC390718 performed important hydrophobic and H-bond interactions with the catalytic residue sites on both targets. The residues that promoted the hydrophobic interactions and H-bonding in the AChE target were Leu67, Trp86, Phe123, Tyr124, Ser293, Phe295, and Tyr341, and on the BuChE target, they were Asp70, Tyr332, Tyr128, Ile442, Trp82, and Glu197. The cytotoxic effect of Z390718, evaluated via cell viability, showed that the molecule has low in vitro toxicity. The in vitro and in silico results indicate that ZINC390718 can be used as chemotype for the optimization and identification of new dual cholinesterase inhibitors.
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56
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Gutiérrez-Mondragón MA, König C, Vellido A. Layer-Wise Relevance Analysis for Motif Recognition in the Activation Pathway of the β2- Adrenergic GPCR Receptor. Int J Mol Sci 2023; 24:ijms24021155. [PMID: 36674669 PMCID: PMC9865744 DOI: 10.3390/ijms24021155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are cell membrane proteins of relevance as therapeutic targets, and are associated to the development of treatments for illnesses such as diabetes, Alzheimer's, or even cancer. Therefore, comprehending the underlying mechanisms of the receptor functional properties is of particular interest in pharmacoproteomics and in disease therapy at large. Their interaction with ligands elicits multiple molecular rearrangements all along their structure, inducing activation pathways that distinctly influence the cell response. In this work, we studied GPCR signaling pathways from molecular dynamics simulations as they provide rich information about the dynamic nature of the receptors. We focused on studying the molecular properties of the receptors using deep-learning-based methods. In particular, we designed and trained a one-dimensional convolution neural network and illustrated its use in a classification of conformational states: active, intermediate, or inactive, of the β2-adrenergic receptor when bound to the full agonist BI-167107. Through a novel explainability-oriented investigation of the prediction results, we were able to identify and assess the contribution of individual motifs (residues) influencing a particular activation pathway. Consequently, we contribute a methodology that assists in the elucidation of the underlying mechanisms of receptor activation-deactivation.
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Affiliation(s)
- Mario A. Gutiérrez-Mondragón
- Computer Science Department, Universitat Politècnica de Catalunya—UPC BarcelonaTech, 08034 Barcelona, Spain
- Intelligent Data Science and Artificial Intelligence (IDEAI-UPC) Research Center, Universitat Politècnica de Catalunya—UPC BarcelonaTech, 08034 Barcelona, Spain
| | - Caroline König
- Computer Science Department, Universitat Politècnica de Catalunya—UPC BarcelonaTech, 08034 Barcelona, Spain
- Intelligent Data Science and Artificial Intelligence (IDEAI-UPC) Research Center, Universitat Politècnica de Catalunya—UPC BarcelonaTech, 08034 Barcelona, Spain
- Correspondence:
| | - Alfredo Vellido
- Computer Science Department, Universitat Politècnica de Catalunya—UPC BarcelonaTech, 08034 Barcelona, Spain
- Intelligent Data Science and Artificial Intelligence (IDEAI-UPC) Research Center, Universitat Politècnica de Catalunya—UPC BarcelonaTech, 08034 Barcelona, Spain
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57
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Najafi V, Yoosefian M, Hassani Z. Development of venetoclax performance using its new derivatives on BCL-2 protein inhibition. Cell Biochem Funct 2023; 41:58-66. [PMID: 36259104 DOI: 10.1002/cbf.3760] [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: 07/23/2022] [Revised: 08/26/2022] [Accepted: 10/04/2022] [Indexed: 01/11/2023]
Abstract
Cancer cells are resistant to apoptosis and this is one of the most obvious symptoms of cancer in humans. One of the most exciting strategies for treating cancer is to design regulators that increase cell death and stop cell growth. Members of the BCL-2 family of proteins play an important role in the regulation of apoptosis. In this study, an attempt was made to improve the performance of one of the anticancer drugs by designing new analogs of venetoclax (VNT). For this purpose, molecular docking studies were performed to determine the best binding state of VNT and its newly designed derivatives at the protein-binding site to estimate the binding energy. The best analog in terms of free energy was VNT-12 with the lowest energy (-12.15 kcal/mol). Finally, to investigate the inhibitory effect of the compounds on BCL-2 protein, molecular dynamics simulation was used, and by performing the relevant analyses during the simulation, it was observed that the newly designed ligand had better performance in inhibiting BCL-2 protein compared to VNT.
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Affiliation(s)
- Vahideh Najafi
- Department of Chemistry, Graduate University of Advanced Technology, Kerman, Iran
| | - Mehdi Yoosefian
- Department of Chemistry, Graduate University of Advanced Technology, Kerman, Iran
| | - Zahra Hassani
- Department of New Materials, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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58
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Zhang H, Luo QQ, Hu ML, Wang N, Qi HZ, Zhang HR, Ding L. Discovery of potent microtubule-destabilizing agents targeting for colchicine site by virtual screening, biological evaluation, and molecular dynamics simulation. Eur J Pharm Sci 2023; 180:106340. [PMID: 36435355 DOI: 10.1016/j.ejps.2022.106340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/03/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022]
Abstract
Microtubule has been considered as attractive therapeutic target for various cancers. Although numerous of chemically diverse compounds targeting to colchicine site have been reported, none of them was approved by Food and Drug Administration. In this investigation, the virtual screening methods, including pharmacophore model, molecular docking, and interaction molecular fingerprints similarity, were applied to discover novel microtubule-destabilizing agents from database with 324,474 compounds. 22 compounds with novel scaffolds were identified as microtubule-destabilizing agents, and then submitted to the biological evaluation. Among these 22 hits, hit4 with novel scaffold represents the best anti-proliferative activity with IC50 ranging from 4.51 to 14.81 μM on four cancer cell lines. The in vitro assays reveal that hit4 can effectively inhibit tubulin assembly, and disrupt the microtubule network in MCF-7 cell at a concentration-dependent manner. Finally, the molecular dynamics simulation analysis exhibits that hit4 can stably bind to colchicine site, interact with key residues, and induce αT5 and βT7 regions changes. The values of ΔGbind for the tubulin-colchicine and tubulin-hit4 are -172.9±10.5 and -166.0±12.6 kJ·mol-1, respectively. The above results indicate that the hit4 is a novel microtubule destabilizing agent targeting to colchicine-binding site, which could be developed as a promising tubulin polymerization inhibitor with higher activity for cancer therapy.
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Affiliation(s)
- Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu 730070, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, PR China.
| | - Qing-Qing Luo
- College of Life Science, Northwest Normal University, Lanzhou, Gansu 730070, PR China
| | - Mei-Ling Hu
- College of Life Science, Northwest Normal University, Lanzhou, Gansu 730070, PR China
| | - Ni Wang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu 730070, PR China
| | - Hua-Zhao Qi
- College of Life Science, Northwest Normal University, Lanzhou, Gansu 730070, PR China
| | - Hong-Rui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu 730070, PR China
| | - Lan Ding
- College of Life Science, Northwest Normal University, Lanzhou, Gansu 730070, PR China
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59
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Kapoor S, Chatterjee DR, Chowdhury MG, Das R, Shard A. Roadmap to Pyruvate Kinase M2 Modulation - A Computational Chronicle. Curr Drug Targets 2023; 24:464-483. [PMID: 36998144 DOI: 10.2174/1389450124666230330103126] [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: 10/01/2022] [Revised: 01/14/2023] [Accepted: 02/10/2023] [Indexed: 04/01/2023]
Abstract
Pyruvate kinase M2 (PKM2) has surfaced as a potential target for anti-cancer therapy. PKM2 is known to be overexpressed in the tumor cells and is a critical metabolic conduit in supplying the augmented bioenergetic demands of the recalcitrant cancer cells. The presence of PKM2 in structurally diverse tetrameric as well as dimeric forms has opened new avenues to design novel modulators. It is also a truism to state that drug discovery has advanced significantly from various computational techniques like molecular docking, virtual screening, molecular dynamics, and pharmacophore mapping. The present review focuses on the role of computational tools in exploring novel modulators of PKM2. The structural features of various isoforms of PKM2 have been discussed along with reported modulators. An extensive analysis of the structure-based and ligand- based in silico methods aimed at PKM2 modulation has been conducted with an in-depth review of the literature. The role of advanced tools like QSAR and quantum mechanics has been established with a brief discussion of future perspectives.
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Affiliation(s)
- Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Ahmedabad, Opposite Air force Station Palaj, Gandhinagar-382355, Gujarat, India
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60
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Menezes Spadeto JP, Freitas MP, Cormanich RA. Fluorinated dihydropyridines as candidates to block L-type voltage-dependent calcium channels. J Biomol Struct Dyn 2022; 40:13456-13471. [PMID: 34720037 DOI: 10.1080/07391102.2021.1989039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Voltage-gated calcium (Cav) channels malfunction may lead to Alzheimer's and cardiovascular disorders, thus a critical protein target for drug development and treatment against several diseases. Indeed, dihydropyridines (DHPs) as nifedipine and amlodipine are top-selling pharmaceuticals and, respectively, the 121st and 5th most prescribed drugs in the United States that have been used as successful selective blockers for L-type Ca2+ channels (LCC) and may be helpful model structures to compare with new DHP analogs. In this context, we have performed a structure-based drug design (SBDD) study of several fluorinated DHPs by using homology modeling, molecular docking, quantitative structure activity relationship (QSAR) and molecular dynamics calculations. Such approaches combined with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) interaction energy results and screening of ADMET (absorption, distribution, metabolism, excretion and toxicity) properties indicate that all ligands in this study are potential new candidates to be tested experimentally for inhibition of LCC and may have higher affinities than the commonly used drugs, being convenient synthetic routes proposed for 11-16, which are among the ligands that showed the best theoretical results concerning LCC inhibition. Furthermore, the ligand interactions with the binding site were carefully examined using the topological noncovalent interactions (NCI) method, which highlighted specifically responsible amino acid residues that increase the spontaneity of the new proposed DHP ligands.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- João Paulo Menezes Spadeto
- Department of Organic Chemistry, Laboratory of Experimental and Theoretical Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, Lavras, MG, Brazil
| | - Rodrigo A Cormanich
- Department of Organic Chemistry, Laboratory of Experimental and Theoretical Organic Chemistry, Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
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61
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Pagba C, Gupta AK, Naji AK, van der Hoeven D, Churion K, Liang X, Jakubec J, Hook M, Zuo Y, Martinez de Kraatz M, Frost JA, Gorfe AA. KRAS Inhibitor that Simultaneously Inhibits Nucleotide Exchange Activity and Effector Engagement. ACS BIO & MED CHEM AU 2022; 2:617-626. [PMID: 37101428 PMCID: PMC10125367 DOI: 10.1021/acsbiomedchemau.2c00045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/27/2022] [Accepted: 09/12/2022] [Indexed: 04/28/2023]
Abstract
We describe a small molecule ligand ACA-14 (2-hydroxy-5-{[(2-phenylcyclopropyl) carbonyl] amino} benzoic acid) as an initial lead for the development of direct inhibitors of KRAS, a notoriously difficult anticancer drug target. We show that the compound binds to KRAS near the switch regions with affinities in the low micromolar range and exerts different effects on KRAS interactions with binding partners. Specifically, ACA-14 impedes the interaction of KRAS with its effector Raf and reduces both intrinsic and SOS-mediated nucleotide exchange rates. Likely as a result of these effects, ACA-14 inhibits signal transduction through the MAPK pathway in cells expressing mutant KRAS and inhibits the growth of pancreatic and colon cancer cells harboring mutant KRAS. We thus propose compound ACA-14 as a useful initial lead for the development of broad-acting inhibitors that target multiple KRAS mutants and simultaneously deplete the fraction of GTP-loaded KRAS while abrogating the effector-binding ability of the already GTP-loaded fraction.
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Affiliation(s)
- Cynthia
V. Pagba
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Amit K. Gupta
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Ali K. Naji
- Department
of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge Street, Houston, Texas 77030, United States
| | - Dharini van der Hoeven
- Department
of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge Street, Houston, Texas 77030, United States
| | - Kelly Churion
- Center
for Infectious and Inflammatory Diseases, Texas A&M University Health Science Center, 2121 W Holcombe Blvd, Houston, Texas 77030, United States
| | - Xiaowen Liang
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Jacob Jakubec
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Magnus Hook
- Center
for Infectious and Inflammatory Diseases, Texas A&M University Health Science Center, 2121 W Holcombe Blvd, Houston, Texas 77030, United States
| | - Yan Zuo
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Marisela Martinez de Kraatz
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Jeffrey A. Frost
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
- Biochemistry
and Cell Biology Program, UTHealth MD Anderson
Cancer Center Graduate School of Biomedical Sciences, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Alemayehu A. Gorfe
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, Texas 77030, United States
- Biochemistry
and Cell Biology Program & Therapeutics and Pharmacology Program, UTHealth MD Anderson Cancer Center Graduate School
of Biomedical Sciences, 6431 Fannin Street, Houston, Texas 77030, United
States
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62
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Emami L, Khabnadideh S, Faghih Z, Farahvasi F, Zonobi F, Gheshlaghi SZ, Daili S, Ebrahimi A, Faghih Z. Synthesis, biological evaluation, and computational studies of some novel quinazoline derivatives as anticancer agents. BMC Chem 2022; 16:100. [PMID: 36419100 PMCID: PMC9682696 DOI: 10.1186/s13065-022-00893-z] [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: 08/23/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022] Open
Abstract
A series of quinazolinone derivatives (7a-7h) were synthesized as antiproliferative agents. All compounds, were synthesized through three steps method and structurally evaluated by FTIR, 1H-NMR, 13CNMR and Mass spectroscopy. Their cytotoxic activities were assessed using MTT protocol against three humans cancerous (MCF-7, A549 and 5637) and normal (MRC-5) cell lines. In addition, molecular docking and simulation studies of the synthesized compounds were performed to assessment their orientation, interaction mode against EGFR as plausible mechanism of quinazoline compounds as anticancer agents. The synthesized compounds mostly showed moderate activity against the three studied cell lines. They also indicated an appropriate selectivity against tumorigenic and non-tumorigenic cell line. The molecular docking results also confirmed biological activity. Most of the compounds fulfilled Lipinski rule. Collectively, these compounds with further modification can be considered as potent antiproliferative agents.
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Affiliation(s)
- Leila Emami
- grid.412571.40000 0000 8819 4698Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran
| | - Soghra Khabnadideh
- grid.412571.40000 0000 8819 4698Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran ,grid.412571.40000 0000 8819 4698Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran
| | - Zahra Faghih
- grid.412571.40000 0000 8819 4698Shiraz Institute for Cancer Research, Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farnoosh Farahvasi
- grid.412571.40000 0000 8819 4698Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran ,grid.412571.40000 0000 8819 4698Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran
| | - Fatemeh Zonobi
- grid.412571.40000 0000 8819 4698Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran ,grid.412571.40000 0000 8819 4698Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran
| | - Saman Zare Gheshlaghi
- grid.412796.f0000 0004 0612 766XDepartment of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Shadi Daili
- grid.17063.330000 0001 2157 2938Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C1A4 Canada
| | - Ali Ebrahimi
- grid.412796.f0000 0004 0612 766XDepartment of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Zeinab Faghih
- grid.412571.40000 0000 8819 4698Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran
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63
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Wu F, Jin S, Jiang Y, Jin X, Tang B, Niu Z, Liu X, Zhang Q, Zeng X, Li SZ. Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203796. [PMID: 36202759 PMCID: PMC9685463 DOI: 10.1002/advs.202203796] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/07/2022] [Indexed: 05/16/2023]
Abstract
The latest biological findings observe that the motionless "lock-and-key" theory is not generally applicable and that changes in atomic sites and binding pose can provide important information for understanding drug binding. However, the computational expenditure limits the growth of protein trajectory-related studies, thus hindering the possibility of supervised learning. A spatial-temporal pre-training method based on the modified equivariant graph matching networks, dubbed ProtMD which has two specially designed self-supervised learning tasks: atom-level prompt-based denoising generative task and conformation-level snapshot ordering task to seize the flexibility information inside molecular dynamics (MD) trajectories with very fine temporal resolutions is presented. The ProtMD can grant the encoder network the capacity to capture the time-dependent geometric mobility of conformations along MD trajectories. Two downstream tasks are chosen to verify the effectiveness of ProtMD through linear detection and task-specific fine-tuning. A huge improvement from current state-of-the-art methods, with a decrease of 4.3% in root mean square error for the binding affinity problem and an average increase of 13.8% in the area under receiver operating characteristic curve and the area under the precision-recall curve for the ligand efficacy problem is observed. The results demonstrate a strong correlation between the magnitude of conformation's motion in the 3D space and the strength with which the ligand binds with its receptor.
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Affiliation(s)
- Fang Wu
- School of EngineeringWestlake UniversityHangzhou310024China
- MindRank AI Ltd.Hangzhou310000China
| | - Shuting Jin
- MindRank AI Ltd.Hangzhou310000China
- School of InformaticsXiamen UniversityXiamen361005China
| | | | | | | | | | - Xiangrong Liu
- School of InformaticsXiamen UniversityXiamen361005China
| | - Qiang Zhang
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterHangzhou311200China
- College of Computer Science and TechnologyZhejiang UniversityHangzhou310013China
| | - Xiangxiang Zeng
- School of Information Science and EngineeringHunan UniversityHunan410082China
| | - Stan Z. Li
- School of EngineeringWestlake UniversityHangzhou310024China
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64
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Baba H, Urano R, Nagai T, Okazaki S. Prediction of self-diffusion coefficients of chemically diverse pure liquids by all-atom molecular dynamics simulations. J Comput Chem 2022; 43:1892-1900. [PMID: 36128785 PMCID: PMC9804551 DOI: 10.1002/jcc.26975] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/05/2023]
Abstract
Molecular self-diffusion coefficients underlie various kinetic properties of the liquids involved in chemistry, physics, and pharmaceutics. In this study, 547 self-diffusion coefficients are calculated based on all-atom molecular dynamics (MD) simulations of 152 diverse pure liquids at various temperatures employing the OPLS4 force field. The calculated coefficients are compared with experimental data (424 extracted from the literature and 123 newly measured by pulsed-field gradient nuclear magnetic resonance). The calculations well agree with the experimental values. The determination coefficient and root mean square error between the observed and calculated logarithmic self-diffusion coefficients of the 547 entries are 0.931 and 0.213, respectively, demonstrating that the MD calculation can be an excellent industrial tool for predicting, for example, molecular transportation in liquids such as the diffusion of active ingredients in biological and pharmaceutical liquids. The self-diffusion coefficients collected in this study are compiled into a database for broad researches including artificial intelligence calculations.
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Affiliation(s)
- Hiromi Baba
- New Modality Research Group, Research DepartmentKyoto R&D Center, Maruho Co., Ltd.KyotoJapan
- Department of Advanced Materials ScienceThe University of TokyoChibaJapan
| | - Ryo Urano
- Research Institute for Interdisciplinary ScienceOkayama UniversityOkayamaJapan
| | - Tetsuro Nagai
- Department of Advanced Materials ScienceThe University of TokyoChibaJapan
- Department of Chemistry, Faculty of ScienceFukuoka UniversityNanakumaJapan
| | - Susumu Okazaki
- Department of Advanced Materials ScienceThe University of TokyoChibaJapan
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65
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Neto MFA, Campos JM, Cerqueira APM, de Lima LR, Da Costa GV, Ramos RDS, Junior JTM, Santos CBR, Leite FHA. Hierarchical Virtual Screening and Binding Free Energy Prediction of Potential Modulators of Aedes Aegypti Odorant-Binding Protein 1. Molecules 2022; 27:molecules27206777. [PMID: 36296371 PMCID: PMC9612181 DOI: 10.3390/molecules27206777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The Aedes aegypti mosquito is the main hematophagous vector responsible for arbovirus transmission in Brazil. The disruption of A. aegypti hematophagy remains one of the most efficient and least toxic methods against these diseases and, therefore, efforts in the research of new chemical entities with repellent activity have advanced due to the elucidation of the functionality of the olfactory receptors and the behavior of mosquitoes. With the growing interest of the pharmaceutical and cosmetic industries in the development of chemical entities with repellent activity, computational studies (e.g., virtual screening and molecular modeling) are a way to prioritize potential modulators with stereoelectronic characteristics (e.g., pharmacophore models) and binding affinity to the AaegOBP1 binding site (e.g., molecular docking) at a lower computational cost. Thus, pharmacophore- and docking-based virtual screening was employed to prioritize compounds from Sigma-Aldrich® (n = 126,851) and biogenic databases (n = 8766). In addition, molecular dynamics (MD) was performed to prioritize the most potential potent compounds compared to DEET according to free binding energy calculations. Two compounds showed adequate stereoelectronic requirements (QFIT > 81.53), AaegOBP1 binding site score (Score > 42.0), volatility and non-toxic properties and better binding free energy value (∆G < −24.13 kcal/mol) compared to DEET ((N,N-diethyl-meta-toluamide)) (∆G = −24.13 kcal/mol).
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Affiliation(s)
- Moysés F. A. Neto
- Laboratório de Quimioinformática e Avaliação Biológica, Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, Brazil
| | - Joaquín M. Campos
- Departamento de Química Farmacéutica y Orgánica, Universidad de Granada, 18071 Granada, Spain
- Biosanitary Institute of Granada (ibs.GRANADA), SAS-University of Granada, 18071 Granada, Spain
| | - Amanda P. M. Cerqueira
- Laboratório de Quimioinformática e Avaliação Biológica, Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, Brazil
| | - Lucio R. de Lima
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68902-280, Brazil
| | - Glauber V. Da Costa
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68902-280, Brazil
| | - Ryan Da S. Ramos
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68902-280, Brazil
| | - Jairo T. Magalhães Junior
- Centro Multidisciplinar, Departamento de Saúde, Universidade Federal do Oeste da Bahia, Barreiras 47100-000, Brazil
| | - Cleydson B. R. Santos
- Laboratório de Modelagem e Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68902-280, Brazil
- Correspondence: (C.B.R.S.); (F.H.A.L.)
| | - Franco H. A. Leite
- Laboratório de Quimioinformática e Avaliação Biológica, Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, Brazil
- Correspondence: (C.B.R.S.); (F.H.A.L.)
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66
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França VLB, Amaral JL, Martins YA, Caetano EWS, Brunaldi K, Freire VN. Characterization of the binding interaction between atrazine and human serum albumin: Fluorescence spectroscopy, molecular dynamics and quantum biochemistry. Chem Biol Interact 2022; 366:110130. [PMID: 36037875 DOI: 10.1016/j.cbi.2022.110130] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
Abstract
Atrazine (ATR), one of the most used herbicides worldwide, causes persistent contamination of water and soil due to its high resistance to degradation. ATR is associated with low fertility and increased risk of prostate cancer in humans, as well as birth defects, low birth weight and premature delivery. Describing ATR binding to human serum albumin (HSA) is clinically relevant to future studies about pharmacokinetics, pharmacodynamics and toxicity of ATR, as albumin is the most abundant carrier protein in plasma and binds important small biological molecules. In this work we characterize, for the first time, the binding of ATR to HSA by using fluorescence spectroscopy and performing simulations using molecular docking, classical molecular dynamics and quantum biochemistry based on density functional theory (DFT). We determine the most likely binding sites of ATR to HSA, highlighting the fatty acid binding site FA8 (located between subdomains IA-IB-IIA and IIB-IIIA-IIIB) as the most important one, and evaluate each nearby amino acid residue contribution to the binding interactions explaining the fluorescence quenching due to ATR complexation with HSA. The stabilization of the ATR/FA8 complex was also aided by the interaction between the atrazine ring and SER454 (hydrogen bond) and LEU481(alkyl interaction).
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Affiliation(s)
- Victor L B França
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil
| | - Jackson L Amaral
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil
| | - Yandara A Martins
- Departament of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Ewerton W S Caetano
- Federal Institute of Education, Science and Technology of Ceará, Fortaleza, 60040-531, Brazil
| | - Kellen Brunaldi
- Departament of Physiological Sciences, State University of Maringá, Maringá, 87020-900, Brazil.
| | - Valder N Freire
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil.
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67
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Palacio-Rodriguez K, Vroylandt H, Stelzl LS, Pietrucci F, Hummer G, Cossio P. Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. J Phys Chem Lett 2022; 13:7490-7496. [PMID: 35939819 DOI: 10.1021/acs.jpclett.2c01807] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Simulations with adaptive time-dependent bias enable an efficient exploration of the conformational space of a system. However, the dynamic information is altered by the bias. Infrequent metadynamics recovers the transition rate of crossing a barrier, if the collective variables are ideal and there is no bias deposition near the transition state. Unfortunately, these conditions are not always fulfilled. To overcome these limitations, and inspired by single-molecule force spectroscopy, we use Kramers' theory for calculating the barrier-crossing rate when a time-dependent bias is added to the system. We assess the efficiency of collective variables parameter by measuring how efficiently the bias accelerates the transitions. We present approximate analytical expressions of the survival probability, reproducing the barrier-crossing time statistics and enabling the extraction of the unbiased transition rate even for challenging cases. We explore the limits of our method and provide convergence criteria to assess its validity.
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Affiliation(s)
- Karen Palacio-Rodriguez
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS UMR 7590, 75005 Paris, France
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia, 050010 Medellín, Colombia
| | - Hadrien Vroylandt
- Institut des sciences du calcul et des données, Sorbonne Université, 75005 Paris, France
| | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- KOMET 1, Institute of Physics, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
- Institute of Molecular Biology, 55128 Mainz, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Fabio Pietrucci
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS UMR 7590, 75005 Paris, France
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Pilar Cossio
- Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia, 050010 Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Center for Computational Mathematics, Flatiron Institute, 10010 New York, United States
- Center for Computational Biology, Flatiron Institute, 10010 New York, United States
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68
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Akkoc S, Karatas H, Muhammed MT, Kökbudak Z, Ceylan A, Almalki F, Laaroussi H, Ben Hadda T. Drug design of new therapeutic agents: molecular docking, molecular dynamics simulation, DFT and POM analyses of new Schiff base ligands and impact of substituents on bioactivity of their potential antifungal pharmacophore site. J Biomol Struct Dyn 2022:1-14. [DOI: 10.1080/07391102.2022.2111360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Senem Akkoc
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Süleyman Demirel University, Isparta, Türkiye
- Faculty of Engineering and Natural Sciences, Bahçeşehir University, Istanbul, Türkiye
| | - Halis Karatas
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, Türkiye
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Süleyman Demirel University, Isparta, Türkiye
| | - Zülbiye Kökbudak
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, Türkiye
| | - Ahmet Ceylan
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Erciyes University, Kayseri, Türkiye
| | - Faisal Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Science, Mohammed Premier University, Oujda, Morocco
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Science, Mohammed Premier University, Oujda, Morocco
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69
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Ferrández MR, Puertas-Martín S, Redondo JL, Pérez-Sánchez H, Ortigosa PM. A two-layer mono-objective algorithm based on guided optimization to reduce the computational cost in virtual screening. Sci Rep 2022; 12:12769. [PMID: 35896716 PMCID: PMC9326156 DOI: 10.1038/s41598-022-16913-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Virtual screening methods focus on searching molecules with similar properties to a given compound. Molecule databases are made up of large numbers of compounds and are constantly increasing. Therefore, fast and efficient methodologies and tools have to be designed to explore them quickly. In this context, ligand-based virtual screening methods are a well-known and helpful tool. These methods focus on searching for the most similar molecules in a database to a reference one. In this work, we propose a new tool called 2L-GO-Pharm, which requires less computational effort than OptiPharm, an efficient and robust piece of software recently proposed in the literature. The new-implemented tool maintains or improves the quality of the solutions found by OptiPharm, and achieves it by considerably reducing the number of evaluations needed. Some of the strengths that help 2L-GO-Pharm enhance searchability are the reduction of the search space dimension and the introduction of some circular limits for the angular variables. Furthermore, to ensure a trade-off between exploration and exploitation of the search space, it implements a two-layer strategy and a guided search procedure combined with a convergence test on the rotation axis. The performance of 2L-GO-Pharm has been tested by considering two different descriptors, i.e. shape similarity and electrostatic potential. The results show that it saves up to 87.5 million evaluations per query molecule.
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Affiliation(s)
- Miriam R Ferrández
- Supercomputing-Algorithms Research Group (SAL), Agrifood Campus of International Excellence, University of Almería, Carretera Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain.
| | - Savíns Puertas-Martín
- Supercomputing-Algorithms Research Group (SAL), Agrifood Campus of International Excellence, University of Almería, Carretera Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain
| | - Juana L Redondo
- Supercomputing-Algorithms Research Group (SAL), Agrifood Campus of International Excellence, University of Almería, Carretera Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain.
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica San Antonio De Murcia (UCAM), Campus de los Jerónimos, 30107, Murcia, Spain
| | - Pilar M Ortigosa
- Supercomputing-Algorithms Research Group (SAL), Agrifood Campus of International Excellence, University of Almería, Carretera Sacramento s/n, La Cañada de San Urbano, 04120, Almería, Spain
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70
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Khabnadideh S, Solhjoo A, Heidari R, Amiri Zirtol L, Sakhteman A, Rezaei Z, Babaei E, Rahimi S, Emami L. Efficient synthesis of 1,3-naphtoxazine derivatives using reusable magnetic catalyst (GO-Fe 3O 4-Ti (IV)): anticonvulsant evaluation and computational studies. BMC Chem 2022; 16:44. [PMID: 35689296 PMCID: PMC9188075 DOI: 10.1186/s13065-022-00836-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/30/2022] [Indexed: 12/29/2022] Open
Abstract
A series of 2-aryl/alkyl-2,3-dihydro-1H-naphtho[1,2-e][1,3]oxazines (S1-S11) were synthesized with an eco-friendly and recoverable nanocatalyst (GO-Fe3O4-Ti(IV)) as an efficient magnetic composite. The new nanocatalyst was characterized by FT-IR, XRD and, EDS analysis. A conformable procedure, easy to work up and having a short reaction time with high yields are some advantages of this method. The new catalyst is also thermal-stable, reusable and, environment-friendly. The chemical structures of the synthesized 1,3-oxazine compounds were confirmed by comparing their melting points with those reported in literature. Then, the anticonvulsant activity of these compounds was assessed by the intraperitoneal pentylenetetrazole test (ipPTZ). Compounds S10 and S11 displayed considerable activity against chemically-induced seizure tests. The molecular simulation was also done to achieve their binding affinities as γ-aminobutyric acid A (GABA-A) receptor agonists as an assumptive mechanism of their anticonvulsant action. The result of molecular studies represented strongly matched with biological activity. Molecular docking simulation of the potent compound (S10) and diazepam as the positive control was performed and some critical residues like Thr262, Asn265, Met286, Phe289, and Val290 were identified. Based on the anticonvulsant results and also in silico ADME predictions, S11 can be to become a potential drug candidate as an anticonvulsant agent.
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Affiliation(s)
- Soghra Khabnadideh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Heidari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Amiri Zirtol
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elaheh Babaei
- Department of Chemistry, College of Science, Yazd University, Yazd, Iran
| | - Samaneh Rahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Salifu EY, Rashid IA, Soliman MES. Impact of compound mutations I1171N + F1174I and I1171N + L1198H on the structure of ALK in NSCLC pathogenesis: atomistic insights. J Biomol Struct Dyn 2022:1-9. [PMID: 35514136 DOI: 10.1080/07391102.2022.2072390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Anaplastic lymphoma kinase (ALK) fusion genes are found in 3%-5% of non-small cell lung cancers (NSCLCs). NSCLC is the most common type of lung cancer, accounting for 84% of all lung cancer diagnoses. Available treatment options for ALK-positive NSCLCs involve the use of ALK tyrosine kinase inhibitors (ALK-TKIs) which have shown to be effective with a high response rate. Nonetheless, the emergence of multiple compound mutations such as I1171N + F1174I or I1171N + L1198H has been reported to cause resistance to all approved ALK-TKIs. However, the underlying molecular mechanisms surrounding the impact of these compound mutants remain poorly understood. Hence, we performed molecular dynamics simulations to characterize the structural effects and functional implications of these compound mutations. Findings revealed a destabilizing effect on ALK by mutants as compared to the wild-type ALK structure. Also, further insights revealed a lower root-mean-squared fluctuation, radius of gyration, and solvent-accessible surface area values of I1171N + F1174I and I1171N + L1198H ALK compound mutations suggesting that the mutants have a more compact structure and a smaller surface area than the wild-type protein. The mutants also distorted the activation loop residues (Tyr1278, Tyr1282, and Tyr1283) in the ALK structure, which further identify them as possible disruptors of phosphorylation. In contrast to wild conformation, the mutant conformations exhibited a reduced node degree in their residue interaction networks. Collectively, our findings provide deeper insights into the deleterious effects of I1171N + F1174I and I1171N + L1198H ALK compound mutations, which may contribute to NSCLC pathogenesis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elliasu Y Salifu
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Issahaku A Rashid
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Loop 422–437 in NanA from Streptococcus pneumoniae plays the role of an active site lid and is associated with allosteric regulation. Comput Biol Med 2022; 144:105290. [DOI: 10.1016/j.compbiomed.2022.105290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 11/03/2022]
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73
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Zhou Y, Jiang Y, Chen SJ. RNA-ligand molecular docking: advances and challenges. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1571. [PMID: 37293430 PMCID: PMC10250017 DOI: 10.1002/wcms.1571] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022]
Abstract
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions has become an indispensable tool for RNA-targeted drug discovery. The current models for RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking and scoring should tackle four crucial problems: (1) conformational flexibility of ligand, (2) conformational flexibility of RNA, (3) efficient sampling of binding sites and binding poses, and (4) accurate scoring of different binding modes. Moreover, compared with the problem of protein-ligand docking, predicting ligand binding to RNA, a negatively charged polymer, is further complicated by additional effects such as metal ion effects. Thermodynamic models based on physics-based and knowledge-based scoring functions have shown highly encouraging success in predicting ligand binding poses and binding affinities. Recently, kinetic models for ligand binding have further suggested that including dissociation kinetics (residence time) in ligand docking would result in improved performance in estimating in vivo drug efficacy. More recently, the rise of deep-learning approaches has led to new tools for predicting RNA-small molecule binding. In this review, we present an overview of the recently developed computational methods for RNA-ligand docking and their advantages and disadvantages.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Yangwei Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
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74
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do Bomfim MR, Barbosa DB, de Carvalho PB, da Silva AM, de Oliveira TA, Taranto AG, Leite FHA. Identification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2069155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mayra Ramos do Bomfim
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Deyse Brito Barbosa
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alisson Marques da Silva
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
| | - Tiago Alves de Oliveira
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Alex Gutterres Taranto
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
- Faculty of Computing, University of Latvia (UL), Riga, Latvia
| | - Franco Henrique Andrade Leite
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
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Silva BM, Santos LH, de Almeida JPP, de Magalhães MTQ. Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches. J Biomol Struct Dyn 2022; 41:3062-3075. [PMID: 35249470 DOI: 10.1080/07391102.2022.2045222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Rad5 protein is an SWI/SNF family ubiquitin ligase that contains an N-terminal HIRAN domain and a RING C3HC4 motif. The HIRAN domain is critical for recognition of the stalled replication fork during the replication process and acts as a sensor to initiate the damaged DNA checkpoint. It is a conserved domain widely distributed in eukaryotic organisms and is present in several DNA-binding proteins from all kingdoms. Here we showed that distant species have important differences in key residues that affect affinity for ssDNA. Based on these findings, we hypothesized that different HIRAN domains might affect fork reversal and translesion synthesis through different metabolic processes. To address this question, we predicted the tertiary structure of both yeast and human HIRAN domains using molecular modeling. Structural dynamics experiments showed that the yeast HIRAN domain exhibited higher structural denaturation than its human homolog, although both domains became stable in the presence of ssDNA. Analysis of atomic contacts revealed that a greater number of interactions between the ssDNA nucleotides and the Rad5 domain are electrostatic. Taken together, these results provide new insights into the molecular mechanism of the HIRAN domain of Rad5 and may guide us to further elucidate differences in the ancient eukaryotes HIRAN sequences and their DNA affinity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bruno M Silva
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Lucianna H Santos
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Molecular Modeling and Drug Planning Laboratory, Department of Biochemistry and Immunology, Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - João Paulo P de Almeida
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
| | - Mariana T Q de Magalhães
- Inter-unit postgraduate studies program in Bioinformatics, Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil.,Macromolecular Biophysics Laboratory (LBM), Biological Sciences Institute (ICB), Federal University of Minas Gerais, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
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Abstract
Drug design is a complex pharmaceutical science with a long history. Many achievements have been made in the field of drug design since the end of 19th century, when Emil Fisher suggested that the drug-receptor interaction resembles the key and lock interplay. Gradually, drug design has been transformed into a coherent and well-organized science with a solid theoretical background and practical applications. Now, drug design is the most advanced approach for drug discovery. It utilizes the innovations in science and technology and includes them in its wide-ranging arsenal of methods and tools in order to achieve the main goal: discovery of effective, specific, non-toxic, safe and well-tolerated drugs. Drug design is one of the most intensively developing modern sciences and its progress is accelerated by the implication of artificial intelligence. The present review aims to capture some of the most important milestones in the development of drug design, to outline some of the most used current methods and to sketch the future perspective according to the author's point of view. Without pretending to cover fully the wide range of drug design topics, the review introduces the reader to the content of Molecules' Special Issue "Drug Design-Science and Practice".
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Affiliation(s)
- Irini Doytchinova
- Drug Design and Bioinformatics Lab, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
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77
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Melagraki G. Reducing health & environmental impacts of chemical warfare agents: Computational chemistry contributions. CHEMOSPHERE 2022; 288:132564. [PMID: 34673043 DOI: 10.1016/j.chemosphere.2021.132564] [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: 07/19/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
This review article summarizes advances in computational chemistry and cheminformatics methods and techniques that are used or have potential for use in reducing health and environmental impacts of Chemical Warfare Agents (CWA). These methods, include, but are not limited to, predictive modeling, data mining and virtual screening, similarity searching, molecular docking and dynamics and are briefly presented here. Applications of these in silico approaches, specifically for the protection of personnel and civilians against CWA, but also beyond, are discussed. CWA include toxic chemicals that can cause death, injury, or temporary incapacitation through their chemical action. CWA impose a significant worldwide threat and as such, destruction, remediation as well as protection measurements need to be carefully designed. Towards this goal computational chemistry and cheminformatics can play a key role specifically as far as decontamination, risk assessment and risk management are concerned. Among the wide range of in silico techniques applied for CWA, specific previously published paradigms are presented, including toxicity and property prediction, CWA simulant identification and CWA detoxification. Beyond CWA research, other applications with military interest are briefly presented and emerging trends of potential relevance noted.
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Affiliation(s)
- Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece.
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Ortiz-Zamora L, Ferreira JV, de Oliveira NKS, de Molfetta FA, Hage-Melim LIS, Fernandes CP, Oliveira AEMFM. Potential implications of vouacapan compounds for insecticidal activity: an in silico study. Recent Pat Biotechnol 2022; 16:155-173. [PMID: 34994338 DOI: 10.2174/1872208316666220106110902] [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: 08/04/2021] [Revised: 08/11/2021] [Accepted: 11/30/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND From the fruits and seeds of the species of Pterodon, it is possible to obtain two main products: the essential oil and oleoresin. In oleoresin, numerous vouacapan compounds have been demonstrated to have biological potential, including insecticidal activity. OBJECTIVE In silico studies were performed to identify potential candidates for natural insecticides among the vouacapans present in the genus Pterodon. MATERIALS AND METHODS Molecular docking and molecular dynamics studies were performed to analyze the interaction of vouacapan compounds with acetylcholinesterase of Drosophila melanogaster. Pharmacokinetic parameters regarding physicochemical properties, plasma protein binding, and activity in the central nervous system were evaluated. The toxicological properties of the selected molecules were predicted using Malathion as the reference compound. RESULTS 6α,7β-dimethoxivouacapan-17-ene (15) showed a high number of interactions and scores in molecular docking studies. This result suggests that this compound exhibits an inhibitory activity of the enzyme acetylcholinesterase. Regarding physicochemical properties, this compound showed the best results, besides presenting low cutaneous permeability values, suggesting null absorption. Molecular dynamics studies demonstrated few conformational changes in the structure of the complex formed by compound 4 and acetylcholinesterase enzyme throughout the simulation time. CONCLUSION It was determined that compound 4 (vouacapan 6α,7β,17β,19-tetraol) is an excellent candidate for usage as a natural insecticide.
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Affiliation(s)
- Lisset Ortiz-Zamora
- Post-Graduate Program in Tropical Biodiversity, Amapá Federal University, Macapá, Amapá, Brazil
- Laboratory of Phytopharmaceutical Nanobiotechnology, Amapá Federal University, Macapá, Amapá, Brazil
| | - Jaderson V Ferreira
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
| | - Nayana K S de Oliveira
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
| | - Fábio A de Molfetta
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Lorane I S Hage-Melim
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Macapá, Amapá, Brazil
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
| | - Caio P Fernandes
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
| | - Anna E M F M Oliveira
- Post-Graduate Program in Pharmaceutical Sciences, Amapá Federal University, Macapá, Amapá, Brazil
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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81
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Salifu EY, Agoni C, Soliman ME. Highlighting the mechanistic role of Olutasidenib (FT-2102) in the selective inhibition of mutated isocitrate dehydrogenase 1 (mIDH1) in cancer therapy. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2021.100829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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82
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Molecular docking and molecular dynamic simulation approaches for drug development and repurposing of drugs for severe acute respiratory syndrome-Coronavirus-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300476 DOI: 10.1016/b978-0-323-91172-6.00007-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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83
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Computer-aided identification of potential inhibitors against Necator americanus glutathione S-transferase 3. INFORMATICS IN MEDICINE UNLOCKED 2022; 30:100957. [PMID: 36570094 PMCID: PMC9784411 DOI: 10.1016/j.imu.2022.100957] [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] [Indexed: 12/30/2022] Open
Abstract
Hookworm infection is caused by the blood-feeding hookworm gastrointestinal nematodes. Its harmful effects include anemia and retarded growth and are common in the tropics. A current control method involves the mass drug administration of synthetic drugs, mainly albendazole and mebendazole. There are however concerns of low efficacy and drug resistance due to their repeated and excessive use. Although, Necator americanus glutathione S-transferase 3 (Na-GST-3) is a notable target, using natural product libraries for computational elucidation of promising leads is underexploited. This study sought to use pharmacoinformatics techniques to identify compounds of natural origins with the potential to be further optimized as promising inhibitors. A compendium of 3182 African natural products together with five known helminth GST inhibitors including Cibacron blue was screened against the active sites of the Na-GST-3 structure (PDB ID: 3W8S). The hit compounds were profiled to ascertain the mechanisms of binding, anthelmintic bioactivity, physicochemical and pharmacokinetic properties. The AutoDock Vina docking protocol was validated by obtaining 0.731 as the area under the curve calculated via the receiver operating characteristics curve. Four compounds comprising ZINC85999636, ZINC35418176, ZINC14825190, and Dammarane Triterpene13 were identified as potential lead compounds with binding energies less than -9.0 kcal/mol. Furthermore, the selected compounds formed key intermolecular interactions with critical residues Tyr95, Gly13 and Ala14. Notably, ZINC85999636, ZINC14825190, and dammarane triterpene13 were predicted as anthelmintics, whilst all the four molecules shared structural similarities with known inhibitors. Molecular modelling showed that the compounds had reasonably good binding free energies. More so, they had high binding affinities when screened against other variants of the Na-GST, namely Na-GST-1 and Na-GST-2. Ligand quality assessment using ligand efficiency dependent lipophilicity, ligand efficiency, ligand efficiency scale and fit quality scale showed the molecules are worthy candidates for further optimization. The inhibitory potentials of the molecules warrant in vitro studies to evaluate their effect on the heme regulation mechanisms.
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84
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Tam NM, Nguyen TH, Ngan VT, Tung NT, Ngo ST. Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211480. [PMID: 35116157 PMCID: PMC8790385 DOI: 10.1098/rsos.211480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The umbrella sampling (US) simulation is demonstrated to be an efficient approach for determining the unbinding pathway and binding affinity to the SARS-CoV-2 Mpro of small molecule inhibitors. The accuracy of US is in the same range as the linear interaction energy (LIE) and fast pulling of ligand (FPL) methods. In detail, the correlation coefficient between US and experiments does not differ from FPL and is slightly smaller than LIE. The root mean square error of US simulations is smaller than that of LIE. Moreover, US is better than FPL and poorer than LIE in classifying SARS-CoV-2 Mpro inhibitors owing to the reciever operating characteristic-area under the curve analysis. Furthermore, the US simulations also provide detailed insights on unbinding pathways of ligands from the binding cleft of SARS-CoV-2 Mpro. The residues Cys44, Thr45, Ser46, Leu141, Asn142, Gly143, Glu166, Leu167, Pro168, Ala191, Gln192 and Ala193 probably play an important role in the ligand dissociation. Therefore, substitutions at these points may change the mechanism of binding of inhibitors to SARS-CoV-2 Mpro.
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Affiliation(s)
- Nguyen Minh Tam
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngan
- Laboratory of Computational Chemistry and Modelling, Department of Chemistry, Quy Nhon University, Quy Nhon, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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85
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Qureshi R, Ghosh A, Yan H. Correlated Motions and Dynamics in Different Domains of Epidermal Growth Factor Receptor With L858R and T790M Mutations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:383-394. [PMID: 32750848 DOI: 10.1109/tcbb.2020.2995569] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Non-small cell lung cancer with an activating epidermal growth factor receptor (EGFR) mutation responds well to targeted drugs. In most cases, drug resistance appears after about a year. Several studies have been conducted on the kinase domain of EGFR to understand the drug resistance mechanism. Since EGFR is a multi-domain protein, mutation in the kinase domain may affect the other domains as well. In this study, we examine the complete structure of the multi-domain EGFR protein and its mutants. We performed molecular dynamics simulations for wildtype EGFR, EGFR with L858R mutation, and EGFR with L858R and T790M mutations. We applied normal mode analysis and complex network analysis to extract the correlated motions in the domains of EGFR. The normal modes are used to construct the dynamic cross-correlation map (DCCM). Simulation results show different patterns of correlated motions in each domain of EGFR mutants compared to the wildtype. In Domains 1 and 3 of the extracellular region, a small number of weak positively correlated motions are extracted. Domains 2 and 4 show large numbers of both positive and negative motions. However, the negatively correlated motions are stronger in mutant structures compared to the wildtype. In Domain 7, some residues showed a positive correlation around the main diagonal. We also identified different communities, nodes and crucial residues in the domains of the structures, which can be important for the function of EGFR. Moreover, hydrogen bond analysis is performed for the stability analysis. The mutant structures have fewer hydrogen bonds compared to the wildtype. Overall, these findings are useful for understanding the dynamics and communications in EGFR domains.
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Lee KE, Bharadwaj S, Sahoo AK, Yadava U, Kang SG. Determination of tyrosinase-cyanidin-3-O-glucoside and (-/+)-catechin binding modes reveal mechanistic differences in tyrosinase inhibition. Sci Rep 2021; 11:24494. [PMID: 34969954 PMCID: PMC8718538 DOI: 10.1038/s41598-021-03569-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Tyrosinase, exquisitely catalyzes the phenolic compounds into brown or black pigment, inhibition is used as a treatment for dermatological or neurodegenerative disorders. Natural products, such as cyanidin-3-O-glucoside and (-/+)-catechin, are considered safe and non-toxic food additives in tyrosinase inhibition but their ambiguous inhibitory mechanism against tyrosinase is still elusive. Thus, we presented the mechanistic insights into tyrosinase with cyanidin-3-O-glucoside and (-/+)-catechin using computational simulations and in vitro assessment. Initial molecular docking results predicted ideal docked poses (- 9.346 to - 5.795 kcal/mol) for tyrosinase with selected flavonoids. Furthermore, 100 ns molecular dynamics simulations and post-simulation analysis of docked poses established their stability and oxidation of flavonoids as substrate by tyrosinase. Particularly, metal chelation via catechol group linked with the free 3-OH group on the unconjugated dihydropyran heterocycle chain was elucidated to contribute to tyrosinase inhibition by (-/+)-catechin against cyanidin-3-O-glucoside. Also, predicted binding free energy using molecular mechanics/generalized Born surface area for each docked pose was consistent with in vitro enzyme inhibition for both mushroom and murine tyrosinases. Conclusively, (-/+)-catechin was observed for substantial tyrosinase inhibition and advocated for further investigation for drug development against tyrosinase-associated diseases.
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Affiliation(s)
- Kyung Eun Lee
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
- Stemforce, 313 Institute of Industrial Technology, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Center, Vestec, Czech Republic.
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211015, Uttar Pradesh, India.
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India.
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, 38541, Gyeongbuk, Korea.
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87
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Kralj S, Jukič M, Bren U. Commercial SARS-CoV-2 Targeted, Protease Inhibitor Focused and Protein-Protein Interaction Inhibitor Focused Molecular Libraries for Virtual Screening and Drug Design. Int J Mol Sci 2021; 23:393. [PMID: 35008818 PMCID: PMC8745317 DOI: 10.3390/ijms23010393] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
Since December 2019, the new SARS-CoV-2-related COVID-19 disease has caused a global pandemic and shut down the public life worldwide. Several proteins have emerged as potential therapeutic targets for drug development, and we sought out to review the commercially available and marketed SARS-CoV-2-targeted libraries ready for high-throughput virtual screening (HTVS). We evaluated the SARS-CoV-2-targeted, protease-inhibitor-focused and protein-protein-interaction-inhibitor-focused libraries to gain a better understanding of how these libraries were designed. The most common were ligand- and structure-based approaches, along with various filtering steps, using molecular descriptors. Often, these methods were combined to obtain the final library. We recognized the abundance of targeted libraries offered and complimented by the inclusion of analytical data; however, serious concerns had to be raised. Namely, vendors lack the information on the library design and the references to the primary literature. Few references to active compounds were also provided when using the ligand-based design and usually only protein classes or a general panel of targets were listed, along with a general reference to the methods, such as molecular docking for the structure-based design. No receptor data, docking protocols or even references to the applied molecular docking software (or other HTVS software), and no pharmacophore or filter design details were given. No detailed functional group or chemical space analyses were reported, and no specific orientation of the libraries toward the design of covalent or noncovalent inhibitors could be observed. All libraries contained pan-assay interference compounds (PAINS), rapid elimination of swill compounds (REOS) and aggregators, as well as focused on the drug-like model, with the majority of compounds possessing their molecular mass around 500 g/mol. These facts do not bode well for the use of the reviewed libraries in drug design and lend themselves to commercial drug companies to focus on and improve.
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Affiliation(s)
- Sebastjan Kralj
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (S.K.); (M.J.)
| | - Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (S.K.); (M.J.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (S.K.); (M.J.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
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Mao J, Luo QQ, Zhang HR, Zheng XH, Shen C, Qi HZ, Hu ML, Zhang H. Discovery of microtubule stabilizers with novel scaffold structures based on virtual screening, biological evaluation, and molecular dynamics simulation. Chem Biol Interact 2021; 352:109784. [PMID: 34932952 DOI: 10.1016/j.cbi.2021.109784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/20/2021] [Accepted: 12/16/2021] [Indexed: 02/08/2023]
Abstract
Disrupting the dynamics and structures of microtubules can perturb mitotic spindle formation, cause cell cycle arrest in G2/M phase, and subsequently lead to cellular death via apoptosis. In this investigation, the structure-based virtual screening methods, including molecular docking and rescoring, and similarity analysis of interaction molecular fingerprints, were developed to discover novel tubulin inhibitors from ChemDiv database with 1,601,806 compounds. The screened compounds were further filtered by PAINS, ADME/T, Toxscore, SAscore, and Drug-likeness analysis. Finally, 17 hit compounds were selected, and then submitted to the biologic evaluation. Among these hits, the P2 exhibited the strongest antiproliferative activity against four tumor cells including HeLa, HepG2, MCF-7, and A549. The in vitro tubulin polymerization assay revealed P2 could promote tubulin polymerization in a dose dependent manner. Finally, in order to analyze the interaction modes of complexes, the molecular dynamics simulation was performed to investigate the interactions between P2 and tubulin. The molecular dynamics simulation analysis showed that P2 could stably bind to taxane site, induced H6-H7, B9-B10, and M-loop regions changes. The ΔGbind energies of tubulin-P2 and tubulin-paclitaxel were -68.25 ± 12.98 and -146.05 ± 16.17 kJ mol-1, respectively, which were in line with the results of the experimental test. Therefore, P2 has been well characterized as lead compounds for developing new tubulin inhibitors with potential anticancer activity.
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Affiliation(s)
- Jun Mao
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Qing-Qing Luo
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hong-Rui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Xiu-He Zheng
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Chen Shen
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hua-Zhao Qi
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Mei-Ling Hu
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, PR China.
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Ma LL, Liu HM, Liu XM, Yuan XY, Xu C, Wang F, Lin JZ, Xu RC, Zhang DK. Screening S protein - ACE2 blockers from natural products: Strategies and advances in the discovery of potential inhibitors of COVID-19. Eur J Med Chem 2021; 226:113857. [PMID: 34628234 PMCID: PMC8489279 DOI: 10.1016/j.ejmech.2021.113857] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/11/2021] [Accepted: 09/15/2021] [Indexed: 02/09/2023]
Abstract
The Coronavirus disease, 2019 (COVID-19) is caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), which poses a major threat to human life and health. Given its continued development, limiting the spread of COVID-19 in the population remains a challenging task. Currently, multiple therapies are being tried around the world to deal with SARS-CoV-2 infection, and a variety of studies have shown that natural products have a significant effect on COVID-19 patients. The combination of SARS-CoV-2 S protein with Angiotensin converting enzyme II(ACE2) of host cell to promote membrane fusion is an initial critical step for SARS-CoV-2 infection. Therefore, screening natural products that inhibit the binding of SARS-CoV-2 S protein and ACE2 also provides a feasible strategy for the treatment of COVID-19. Establishment of high throughput screening model is an important basis and key technology for screening S protein-ACE2 blockers. Based on this, the molecular structures of SARS-CoV-2 and ACE2 and their processes in the life cycle of SARS-CoV-2 and host cell infection were firstly reviewed in this paper, with emphasis on the methods and techniques of screening S protein-ACE2 blockers, including Virtual Screening (VS), Surface Plasmon Resonance (SPR), Biochromatography, Biotin-avidin with Enzyme-linked Immunosorbent assay and Gene Chip Technology. Furthermore, the technical principle, advantages and disadvantages and application scope were further elaborated. Combined with the application of the above screening technologies in S protein-ACE2 blockers, a variety of natural products, such as flavonoids, terpenoids, phenols, alkaloids, were summarized, which could be used as S protein-ACE2 blockers, in order to provide ideas for the efficient discovery of S protein-ACE2 blockers from natural sources and contribute to the development of broad-spectrum anti coronavirus drugs.
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Affiliation(s)
- Le-le Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Hui-Min Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Xue-Mei Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Xiao-Yu Yuan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Chao Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Fang Wang
- Key Laboratory of Modern Chinese Medicine Preparation of Ministry of Education, Jiangxi University of Traditional Chinese Medicine Central Laboratory, Nanchang, 330000, PR China
| | - Jun-Zhi Lin
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, PR China.
| | - Run-Chun Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
| | - Ding-Kun Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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Kwofie SK, Broni E, Yunus FU, Nsoh J, Adoboe D, Miller WA, Wilson MD. Molecular Docking Simulation Studies Identifies Potential Natural Product Derived-Antiwolbachial Compounds as Filaricides against Onchocerciasis. Biomedicines 2021; 9:biomedicines9111682. [PMID: 34829911 PMCID: PMC8615632 DOI: 10.3390/biomedicines9111682] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Onchocerciasis is the leading cause of blindness and severe skin lesions which remain a major public health problem, especially in tropical areas. The widespread use of antibiotics and the long duration required for effective treatment continues to add to the increasing global menace of multi-resistant pathogens. Onchocerca volvulus harbors the endosymbiont bacteria Wolbachia, essential for the normal development of embryos, larvae and long-term survival of the adult worm, O. volvulus. We report here results of using structure-based drug design (SBDD) approach aimed at identifying potential novel Wolbachia inhibitors from natural products against the Wolbachia surface protein (WSP). The protein sequence of the WSP with UniProtKB identifier Q0RAI4 was used to model the three-dimensional (3D) structure via homology modelling techniques using three different structure-building algorithms implemented in Modeller, I-TASSER and Robetta. Out of the 15 generated models of WSP, one was selected as the most reasonable quality model which had 82, 15.5, 1.9 and 0.5% of the amino acid residues in the most favored regions, additionally allowed regions, generously allowed regions and disallowed regions, respectively, based on the Ramachandran plot. High throughput virtual screening was performed via Autodock Vina with a library comprising 42,883 natural products from African and Chinese databases, including 23 identified anti-Onchocerca inhibitors. The top six compounds comprising ZINC000095913861, ZINC000095486235, ZINC000035941652, NANPDB4566, acetylaleuritolic acid and rhemannic acid had binding energies of −12.7, −11.1, −11.0, −11, −10.3 and −9.5 kcal/mol, respectively. Molecular dynamics simulations including molecular mechanics Poisson-Boltzmann (MMPBSA) calculations reinforced the stability of the ligand-WSP complexes and plausible binding mechanisms. The residues Arg45, Tyr135, Tyr148 and Phe195 were predicted as potential novel critical residues required for ligand binding in pocket 1. Acetylaleuritolic acid and rhemannic acid (lantedene A) have previously been shown to possess anti-onchocercal activity. This warrants the need to evaluate the anti-WSP activity of the identified molecules. The study suggests the exploitation of compounds which target both pockets 1 and 2, by investigating their potential for effective depletion of Wolbachia. These compounds were predicted to possess reasonably good pharmacological profiles with insignificant toxicity and as drug-like. The compounds were computed to possess biological activity including antibacterial, antiparasitic, anthelmintic and anti-rickettsials. The six natural products are potential novel antiwolbachial agents with insignificant toxicities which can be explored further as filaricides for onchocerciasis.
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Affiliation(s)
- Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Correspondence: ; Tel.: +233-203-797922
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra LG 581, Ghana;
| | - Faruk U. Yunus
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
| | - John Nsoh
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
| | - Dela Adoboe
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, IL 19104, USA
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra LG 581, Ghana;
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
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91
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Şterbuleac D. Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators. RSC Med Chem 2021; 12:1503-1518. [PMID: 34671734 PMCID: PMC8459385 DOI: 10.1039/d1md00140j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/21/2021] [Indexed: 01/10/2023] Open
Abstract
Molecular dynamics (MD) simulations allow researchers to investigate the behavior of desired biological targets at ever-decreasing costs with ever-increasing precision. Among the biological macromolecules, ion channels are remarkable transmembrane proteins, capable of performing special biological processes and revealing a complex regulatory matrix, including modulation by small molecules, either endogenous or exogenous. Recently, given the developments in ion channel structure determination and accessibility of bio-computational techniques, MD and related tools are becoming increasingly popular in the intense research area regarding ligand-channel interactions. This review synthesizes and presents the most important fields of MD involvement in investigating channel-molecule interactions, including, but not limited to, deciphering the binding modes of ligands to their ion channel targets and the mechanisms through which chemical compounds exert their effect on channel function. Special attention is devoted to the importance of more elaborate methods, such as free energy calculations, while principles regarding drug design and discovery are highlighted. Several technical aspects involving the creation and simulation of channel-molecule MD systems (ligand parameterization, proper membrane setup, system building, etc.) are also presented.
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Affiliation(s)
- Daniel Şterbuleac
- Department of Health and Human Development, "Ştefan cel Mare" University of Suceava Str. Universităţii 13, 720229, E Building Suceava Romania
- Department of Forestry and Environmental Protection, "Ştefan cel Mare" University of Suceava Str. Universităţii 13, 720229, E Building Suceava Romania
- Integrated Center for Research, Development and Innovation in Advanced Materials, Nanotechnologies and Distributed Systems for Fabrication and Control (MANSiD), "Ştefan cel Mare" University of Suceava Str. Universităţii 13 720229 Suceava Romania
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92
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Titov IY, Stroylov VS, Rusina P, Svitanko IV. Preliminary modelling as the first stage of targeted organic synthesis. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to present a classification and applicability analysis of methods for preliminary molecular modelling for targeted organic, catalytic and biocatalytic synthesis. The following three main approaches are considered as a primary classification of the methods: modelling of the target – ligand coordination without structural information on both the target and the resulting complex; calculations based on experimentally obtained structural information about the target; and dynamic simulation of the target – ligand complex and the reaction mechanism with calculation of the free energy of the reaction. The review is meant for synthetic chemists to be used as a guide for building an algorithm for preliminary modelling and synthesis of structures with specified properties.
The bibliography includes 353 references.
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93
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Kleandrova VV, Speck-Planche A. The QSAR Paradigm in Fragment-Based Drug Discovery: From the Virtual Generation of Target Inhibitors to Multi-Scale Modeling. Mini Rev Med Chem 2021; 20:1357-1374. [PMID: 32013845 DOI: 10.2174/1389557520666200204123156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
Abstract
Fragment-Based Drug Design (FBDD) has established itself as a promising approach in modern drug discovery, accelerating and improving lead optimization, while playing a crucial role in diminishing the high attrition rates at all stages in the drug development process. On the other hand, FBDD has benefited from the application of computational methodologies, where the models derived from the Quantitative Structure-Activity Relationships (QSAR) have become consolidated tools. This mini-review focuses on the evolution and main applications of the QSAR paradigm in the context of FBDD in the last five years. This report places particular emphasis on the QSAR models derived from fragment-based topological approaches to extract physicochemical and/or structural information, allowing to design potentially novel mono- or multi-target inhibitors from relatively large and heterogeneous databases. Here, we also discuss the need to apply multi-scale modeling, to exemplify how different datasets based on target inhibition can be simultaneously integrated and predicted together with other relevant endpoints such as the biological activity against non-biomolecular targets, as well as in vitro and in vivo toxicity and pharmacokinetic properties. In this context, seminal papers are briefly analyzed. As huge amounts of data continue to accumulate in the domains of the chemical, biological and biomedical sciences, it has become clear that drug discovery must be viewed as a multi-scale optimization process. An ideal multi-scale approach should integrate diverse chemical and biological data and also serve as a knowledge generator, enabling the design of potentially optimal chemicals that may become therapeutic agents.
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Affiliation(s)
- Valeria V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe Shosse 11, 125080, Moscow, Russian Federation
| | - Alejandro Speck-Planche
- Department of Chemistry, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, b. 2, 119992, Moscow, Russian Federation
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94
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Pourhatami A, Kaviyani-Charati M, Kargar B, Baziyad H, Kargar M, Olmeda-Gómez C. Mapping the intellectual structure of the coronavirus field (2000-2020): a co-word analysis. Scientometrics 2021; 126:6625-6657. [PMID: 34149117 PMCID: PMC8204734 DOI: 10.1007/s11192-021-04038-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 05/08/2021] [Indexed: 12/26/2022]
Abstract
Over the two last decades, coronaviruses have affected human life in different ways, especially in terms of health and economy. Due to the profound effects of novel coronaviruses, growing tides of research are emerging in various research fields. This paper employs a co-word analysis approach to map the intellectual structure of the coronavirus literature for a better understanding of how coronavirus research and the disease itself have developed during the target timeframe. A strategic diagram has been drawn to depict the coronavirus domain's structure and development. A detailed picture of coronavirus literature has been extracted from a huge number of papers to provide a quick overview of the coronavirus literature. The main themes of past coronavirus-related publications are (a) "Antibody-Virus Interactions," (b) "Emerging Infectious Diseases," (c) "Protein Structure-based Drug Design and Antiviral Drug Discovery," (d) "Coronavirus Detection Methods," (e) "Viral Pathogenesis and Immunity," and (f) "Animal Coronaviruses." The emerging infectious diseases are mostly related to fatal diseases (such as Middle East respiratory syndrome, severe acute respiratory syndrome, and COVID-19) and animal coronaviruses (including porcine, turkey, feline, canine, equine, and bovine coronaviruses and infectious bronchitis virus), which are capable of placing animal-dependent industries such as the swine and poultry industries under strong economic pressure. Although considerable research into coronavirus has been done, this unique field has not yet matured sufficiently. Therefore, "Antibody-virus Interactions," "Emerging Infectious Diseases," and "Coronavirus Detection Methods" hold interesting, promising research gaps to be both explored and filled in the future.
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Affiliation(s)
- Aliakbar Pourhatami
- Department of Information Technology, Faculty of Industrial and Systems Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Bahareh Kargar
- School of Industrial Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Hamed Baziyad
- Department of Information Technology, Faculty of Industrial and Systems Engineering, Tarbiat Modares University, Tehran, Iran
| | - Maryam Kargar
- School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Carlos Olmeda-Gómez
- Department Library & Information Science, Carlos III University, Madrid, Spain
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95
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Rayka M, Karimi-Jafari MH, Firouzi R. ET-score: Improving Protein-ligand Binding Affinity Prediction Based on Distance-weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm. Mol Inform 2021; 40:e2060084. [PMID: 34021703 DOI: 10.1002/minf.202060084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022]
Abstract
The molecular docking simulation is a key computational tool in modern drug discovery research that its predictive performance strongly depends on the employed scoring functions. Many recent studies have shown that the application of machine learning algorithms in the development of scoring functions has led to a significant improvement in docking performance. In this work, we introduce a new machine learning (ML) based scoring function called ET-Score, which employs the distance-weighted interatomic contacts between atom type pairs of the ligand and the protein for featurizing protein-ligand complexes and Extremely Randomized Trees algorithm for the training process. The performance of ET-Score is compared with some successful ML-based scoring functions and several popular classical scoring functions on the PDBbind 2016v core set. It is shown that our ET-Score model (with Pearson's correlation of 0.827 and RMSE of 1.332) achieves very good performance in comparison with most of the ML-based scoring functions and all classical scoring functions despite its extremely low computational cost. ET-Score's codes are freely available on the web at https://github.com/miladrayka/ET_Score.
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Affiliation(s)
- Milad Rayka
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | | | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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96
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Bharadwaj S, Dubey A, Kamboj NK, Sahoo AK, Kang SG, Yadava U. Drug repurposing for ligand-induced rearrangement of Sirt2 active site-based inhibitors via molecular modeling and quantum mechanics calculations. Sci Rep 2021; 11:10169. [PMID: 33986372 PMCID: PMC8119977 DOI: 10.1038/s41598-021-89627-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
Sirtuin 2 (Sirt2) nicotinamide adenine dinucleotide-dependent deacetylase enzyme has been reported to alter diverse biological functions in the cells and onset of diseases, including cancer, aging, and neurodegenerative diseases, which implicate the regulation of Sirt2 function as a potential drug target. Available Sirt2 inhibitors or modulators exhibit insufficient specificity and potency, and even partially contradictory Sirt2 effects were described for the available inhibitors. Herein, we applied computational screening and evaluation of FDA-approved drugs for highly selective modulation of Sirt2 activity via a unique inhibitory mechanism as reported earlier for SirReal2 inhibitor. Application of stringent molecular docking results in the identification of 48 FDA-approved drugs as selective putative inhibitors of Sirt2, but only top 10 drugs with docking scores > - 11 kcal/mol were considered in reference to SirReal2 inhibitor for computational analysis. The molecular dynamics simulations and post-simulation analysis of Sirt2-drug complexes revealed substantial stability for Fluphenazine and Nintedanib with Sirt2. Additionally, developed 3D-QSAR-models also support the inhibitory potential of drugs, which exclusively revealed highest activities for Nintedanib (pIC50 ≥ 5.90 µM). Conclusively, screened FDA-approved drugs were advocated as promising agents for Sirt2 inhibition and required in vitro investigation for Sirt2 targeted drug development.
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Affiliation(s)
- Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus Pvt. Ltd., Kushinagar, 274203, India
| | - Nitin Kumar Kamboj
- School of Physical Sciences, DIT University, Dehradun, UK, 248001, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, 211015, India.
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India.
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Abstract
Human cytochrome P450 1B1 (CYP1B1) is an extrahepatic heme-containing monooxygenase. CYP1B1 contributes to the oxidative metabolism of xenobiotics, drugs, and endogenous substrates like melatonin, fatty acids, steroid hormones, and retinoids, which are involved in diverse critical cellular functions. CYP1B1 plays an important role in the pathogenesis of cardiovascular diseases, hormone-related cancers and is responsible for anti-cancer drug resistance. Inhibition of CYP1B1 activity is considered as an approach in cancer chemoprevention and cancer chemotherapy. CYP1B1 can activate anti-cancer prodrugs in tumor cells which display overexpression of CYP1B1 in comparison to normal cells. CYP1B1 involvement in carcinogenesis and cancer progression encourages investigation of CYP1B1 interactions with its ligands: substrates and inhibitors. Computational methods, with a simulation of molecular dynamics (MD), allow the observation of molecular interactions at the binding site of CYP1B1, which are essential in relation to the enzyme’s functions.
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98
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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99
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Miroshnychenko KV, Shestopalova AV. Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study. J Biomol Struct Dyn 2021; 40:8672-8686. [PMID: 33896392 PMCID: PMC8074653 DOI: 10.1080/07391102.2021.1914168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
The worldwide rapid spread of the COVID-19 disease necessitates the search for fast and effective treatments. The repurposing of existing drugs seems to be the best solution in this situation. In this study, the molecular docking method was used to test 248 drugs against the receptor-binding domain (RBD) of spike glycoprotein of SARS-CoV-2, which is responsible for viral entry into the host cell. Among the top-ranked ligands are drugs that are used for hepatitis C virus (HCV) treatments (paritaprevir, ledipasvir, simeprevir) and a natural biflavonoid amentoflavone. The binding sites of the HCV drugs and amentoflavone are different. Therefore, the ternary complexes of the HCV drug, amentoflavone, and RBD can be created. For the 5 top-ranked ligands, the validating molecular dynamics simulations of binary and ternary complexes with RBD were performed. According to the MMPBSA-binding free energies, the HCV drugs ledipasvir and paritaprevir (in a neutral form) are the most efficient binders of the RBD when used in combination with amentoflavone.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Anna V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics of NAS of Ukraine, Kharkiv, Ukraine
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
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100
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Bepari AK, Reza HM. Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation. PeerJ 2021; 9:e11261. [PMID: 33954055 PMCID: PMC8051358 DOI: 10.7717/peerj.11261] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has ravaged lives across the globe since December 2019, and new cases are still on the rise. Peoples’ ongoing sufferings trigger scientists to develop safe and effective remedies to treat this deadly viral disease. While repurposing the existing FDA-approved drugs remains in the front line, exploring drug candidates from synthetic and natural compounds is also a viable alternative. This study employed a comprehensive computational approach to screen inhibitors for SARS-CoV-2 3CL-PRO (also known as the main protease), a prime molecular target to treat coronavirus diseases. Methods We performed 100 ns GROMACS molecular dynamics simulations of three high-resolution X-ray crystallographic structures of 3CL-PRO. We extracted frames at 10 ns intervals to mimic conformational diversities of the target protein in biological environments. We then used AutoDock Vina molecular docking to virtual screen the Sigma–Aldrich MyriaScreen Diversity Library II, a rich collection of 10,000 druglike small molecules with diverse chemotypes. Subsequently, we adopted in silico computation of physicochemical properties, pharmacokinetic parameters, and toxicity profiles. Finally, we analyzed hydrogen bonding and other protein-ligand interactions for the short-listed compounds. Results Over the 100 ns molecular dynamics simulations of 3CL-PRO’s crystal structures, 6LZE, 6M0K, and 6YB7, showed overall integrity with mean Cα root-mean-square deviation (RMSD) of 1.96 (±0.35) Å, 1.98 (±0.21) Å, and 1.94 (±0.25) Å, respectively. Average root-mean-square fluctuation (RMSF) values were 1.21 ± 0.79 (6LZE), 1.12 ± 0.72 (6M0K), and 1.11 ± 0.60 (6YB7). After two phases of AutoDock Vina virtual screening of the MyriaScreen Diversity Library II, we prepared a list of the top 20 ligands. We selected four promising leads considering predicted oral bioavailability, druglikeness, and toxicity profiles. These compounds also demonstrated favorable protein-ligand interactions. We then employed 50-ns molecular dynamics simulations for the four selected molecules and the reference ligand 11a in the crystallographic structure 6LZE. Analysis of RMSF, RMSD, and hydrogen bonding along the simulation trajectories indicated that S51765 would form a more stable protein-ligand complexe with 3CL-PRO compared to other molecules. Insights into short-range Coulombic and Lennard-Jones potentials also revealed favorable binding of S51765 with 3CL-PRO. Conclusion We identified a potential lead for antiviral drug discovery against the SARS-CoV-2 main protease. Our results will aid global efforts to find safe and effective remedies for COVID-19.
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Affiliation(s)
- Asim Kumar Bepari
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
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