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El Yaagoubi OM, Ezzemani W, Oularbi L, Samaki H, Aboudkhil S. In silico identification of 20S proteasome-β5 subunit inhibitors using structure-based virtual screening. J Biomol Struct Dyn 2024; 42:6165-6173. [PMID: 37403265 DOI: 10.1080/07391102.2023.2232041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 06/26/2023] [Indexed: 07/06/2023]
Abstract
Proteasome inhibitors have effective anti-tumor activity in cell culture and can induce apoptosis by interfering with the degradation of cell cycle proteins. 20S Proteasome is acknowledged to be a satisfactory target that has persistent properties against the human immune defense and is obligatory for the degradation of some vital proteins. This study aimed to identify potential inhibitors against 20S proteasome, specifically the β5 subunit, using structure-based virtual screening and molecular docking to reduce the number of ligands that should be eligible for experimental assays. A total of 4961 molecules with anticancer activity were screened from the ASINEX database. The filtered compounds that showed higher docking affinity were then used in more sophisticated molecular docking simulations with AutoDock Vina for validation. Finally, six drug molecules (BDE 28974746, BDE 25657353, BDE 29746159, BDD 27844484, BDE 29746109, and BDE 29746162) exhibited highly significant interactions compared to the positive controls were retained. Among these six molecules, three molecules (BDE 28974746, BDE 25657353, and BDD 27844484) showed high binding affinity and binding energy compared with Carfilzomib and Bortezomib. Molecular simulation and dynamics studies of the top three drug molecules in each case allowed us to draw further conclusions about their stability with the β5 subunit. Computed absorption, distribution, metabolism, excretion and toxicity studies on these derivatives showed encouraging results with very low toxicity, distribution, and absorption. These compounds may serve as potential hits for further biological evaluation in the development of new proteasome inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ouadie Mohamed El Yaagoubi
- Laboratory of Biochemistry, Environment and Agri-Food (URAC 36), Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
| | - Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Département de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Larbi Oularbi
- Laboratory of Materials Membranes and Environment, Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
- Supramolecular Nanomaterials Group (SNG), Mohammed VI Polytechnic University (UM6P), Lot 660, HayMoulayRachid, BenGuerir, Morocco
| | - Hamid Samaki
- National Institute of Social Action (INAS), Tangier, Morocco
| | - Souad Aboudkhil
- Laboratory of Biochemistry, Environment and Agri-Food (URAC 36), Faculty of Sciences and Techniques-Mohammedia, Hassan II University of Casablanca, Morocco
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2
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Georgiou N, Karta D, Cheilari A, Merzel F, Tzeli D, Vassiliou S, Mavromoustakos T. Synthesis of Thiazolidin-4-Ones Derivatives, Evaluation of Conformation in Solution, Theoretical Isomerization Reaction Paths and Discovery of Potential Biological Targets. Molecules 2024; 29:2458. [PMID: 38893334 PMCID: PMC11173912 DOI: 10.3390/molecules29112458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Thiazolin-4-ones and their derivatives represent important heterocyclic scaffolds with various applications in medicinal chemistry. For that reason, the synthesis of two 5-substituted thiazolidin-4-one derivatives was performed. Their structure assignment was conducted by NMR experiments (2D-COSY, 2D-NOESY, 2D-HSQC and 2D-HMBC) and conformational analysis was conducted through Density Functional Theory calculations and 2D-NOESY. Conformational analysis showed that these two molecules adopt exo conformation. Their global minimum structures have two double bonds (C=N, C=C) in Z conformation and the third double (C=N) in E. Our DFT results are in agreement with the 2D-NMR measurements. Furthermore, the reaction isomerization paths were studied via DFT to check the stability of the conformers. Finally, some potential targets were found through the SwissADME platform and docking experiments were performed. Both compounds bind strongly to five macromolecules (triazoloquinazolines, mglur3, Jak3, Danio rerio HDAC6 CD2, acetylcholinesterase) and via SwissADME it was found that these two molecules obey Lipinski's Rule of Five.
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Affiliation(s)
- Nikitas Georgiou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (S.V.)
| | - Danai Karta
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (S.V.)
| | - Antigoni Cheilari
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece;
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 11635 Athens, Greece
| | - Stamatia Vassiliou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (S.V.)
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece; (N.G.); (D.K.); (S.V.)
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3
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Zhang Y, Ge G, Xu X, Wu J. Ensemble-Based Virtual Screening Led to the Discovery of Novel Lead Molecules as Potential NMBAs. Molecules 2024; 29:1955. [PMID: 38731447 PMCID: PMC11085220 DOI: 10.3390/molecules29091955] [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: 03/20/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Neuromuscular blocking agents (NMBAs) are routinely used during anesthesia to relax skeletal muscle. Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels; NMBAs can induce muscle paralysis by preventing the neurotransmitter acetylcholine (ACh) from binding to nAChRs situated on the postsynaptic membranes. Despite widespread efforts, it is still a great challenge to find new NMBAs since the introduction of cisatracurium in 1995. In this work, an effective ensemble-based virtual screening method, including molecular property filters, 3D pharmacophore model, and molecular docking, was applied to discover potential NMBAs from the ZINC15 database. The results showed that screened hit compounds had better docking scores than the reference compound d-tubocurarine. In order to further investigate the binding modes between the hit compounds and nAChRs at simulated physiological conditions, the molecular dynamics simulation was performed. Deep analysis of the simulation results revealed that ZINC257459695 can stably bind to nAChRs' active sites and interact with the key residue Asp165. The binding free energies were also calculated for the obtained hits using the MM/GBSA method. In silico ADMET calculations were performed to assess the pharmacokinetic properties of hit compounds in the human body. Overall, the identified ZINC257459695 may be a promising lead compound for developing new NMBAs as an adjunct to general anesthesia, necessitating further investigations.
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Affiliation(s)
- Yi Zhang
- School of Medicine, Nanjing University, Nanjing 210093, China
- Jiangsu Key Laboratory of Central Nervous System Drug Research and Development, Jiangsu Nhwa Pharmaceutical Co., Ltd., Xuzhou 221116, China
| | - Gonghui Ge
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Xiangyang Xu
- Jiangsu Key Laboratory of Central Nervous System Drug Research and Development, Jiangsu Nhwa Pharmaceutical Co., Ltd., Xuzhou 221116, China
| | - Jinhui Wu
- School of Medicine, Nanjing University, Nanjing 210093, China
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4
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Ponnusamy N, Pillai G, Arumugam M. Computational investigation of phytochemicals identified from medicinal plant extracts against tuberculosis. J Biomol Struct Dyn 2024; 42:3382-3395. [PMID: 37211911 DOI: 10.1080/07391102.2023.2213341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/05/2023] [Indexed: 05/23/2023]
Abstract
Tuberculosis (TB) is still one of the world's most challenging infectious diseases and the emergence of drug-resistant Mycobacterium tuberculosis poses a significant threat to the treatment of TB. Identifying new medications based on local traditional remedies has become more essential. Gas Chromatography-Mass spectrometry (GC-MS) (Perkin-Elmer, MA, USA) was used to identify potential bioactive components in Solanum surattense, Piper longum, and Alpinia galanga plants sections. The fruits and rhizomes' chemical compositions were analyzed using solvents like petroleum ether, chloroform, ethyl acetate, and methanol. A total of 138 phytochemicals were identified, further categorized and finalized with 109 chemicals. The phytochemicals were docked with selected proteins (ethA, gyrB, and rpoB) using AutoDock Vina. The top complexes were selected and preceded with molecular dynamics simulation. It was found that the rpoB-sclareol complex is very stable, which means it could be further explored. The compounds were further studied for ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties. Sclareol has obeyed all the rules and it might be a potential chemical to treat TB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nirmaladevi Ponnusamy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | | | - Mohanapriya Arumugam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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5
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Nam Y, Prajapati R, Kim S, Shin SJ, Cheong DY, Park YH, Park HH, Lim D, Yoon Y, Lee G, Jung HA, Park I, Kim DH, Choi JS, Moon M. Dual regulatory effects of neferine on amyloid-β and tau aggregation studied by in silico, in vitro, and lab-on-a-chip technology. Biomed Pharmacother 2024; 172:116226. [PMID: 38301421 DOI: 10.1016/j.biopha.2024.116226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/15/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
Alzheimer's disease (AD) is characterized by the presence of two critical pathogenic factors: amyloid-β (Aβ) and tau. Aβ and tau become neurotoxic aggregates via self-assembly, and these aggregates contribute to the pathogenesis of AD. Therefore, there has been growing interest in therapeutic strategies that simultaneously target Aβ and tau aggregates. Although neferine has attracted attention as a suitable candidate agent for alleviating AD pathology, there has been no study investigating whether neferine affects the modulation of Aβ or tau aggregation/dissociation. Herein, we investigated the dual regulatory effects of neferine on Aβ and tau aggregation/dissociation. We predicted the binding characteristics of neferine to Aβ and tau using molecular docking simulations. Next, thioflavin T and atomic force microscope analyses were used to evaluate the effects of neferine on the aggregation or dissociation of Aβ42 and tau K18. We verified the effect of neferine on Aβ fibril degradation using a microfluidic device. In addition, molecular dynamics simulation was used to predict a conformational change in the Aβ42-neferine complex. Moreover, we examined the neuroprotective effect of neferine against neurotoxicity induced by Aβ and tau and their fibrils in HT22 cells. Finally, we foresaw the pharmacokinetic properties of neferine. These results demonstrated that neferine, which has attracted attention as a potential treatment for AD, can directly affect Aβ and tau pathology.
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Affiliation(s)
- Yunkwon Nam
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Ritu Prajapati
- Department of Food and Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Sujin Kim
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Soo Jung Shin
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Yong Ho Park
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Hyun Ha Park
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea
| | - Danyou Lim
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea
| | - Yoojeong Yoon
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Hyun Ah Jung
- Department of Food Science and Human Nutrition, Chonbuk National University, Jeonju 54896, Republic of Korea
| | - Insu Park
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, Republic of Korea.
| | - Dong-Hyun Kim
- Departments of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea.
| | - Jae Sue Choi
- Department of Food and Life Science, Pukyong National University, Busan 48513, Republic of Korea.
| | - Minho Moon
- Department of Biochemistry, College of Medicine, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea; Research Institute for Dementia Science, Konyang University, 158, Gwanjeodong-ro, Seo-gu, Daejeon 35365, Republic of Korea.
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6
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Georgiou N, Kakava MG, Routsi EA, Petsas E, Stavridis N, Freris C, Zoupanou N, Moschovou K, Kiriakidi S, Mavromoustakos T. Quercetin: A Potential Polydynamic Drug. Molecules 2023; 28:8141. [PMID: 38138630 PMCID: PMC10745404 DOI: 10.3390/molecules28248141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
The study of natural products as potential drug leads has gained tremendous research interest. Quercetin is one of those natural products. It belongs to the family of flavonoids and, more specifically, flavonols. This review summarizes the beneficial pharmaceutical effects of quercetin, such as its anti-cancer, anti-inflammatory, and antimicrobial properties, which are some of the quercetin effects described in this review. Nevertheless, quercetin shows poor bioavailability and low solubility. For this reason, its encapsulation in macromolecules increases its bioavailability and therefore pharmaceutical efficiency. In this review, a brief description of the different forms of encapsulation of quercetin are described, and new ones are proposed. The beneficial effects of applying new pharmaceutical forms of nanotechnology are outlined.
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Affiliation(s)
- Nikitas Georgiou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Margarita Georgia Kakava
- Laboratory of Organic Chemistry and Biochemistry, Department of Chemistry, University of Patras, 26504 Patras, Greece;
| | - Efthymios Alexandros Routsi
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
- Center of Excellence for Drug Design and Discovery, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Errikos Petsas
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Nikolaos Stavridis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Christoforos Freris
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Nikoletta Zoupanou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Kalliopi Moschovou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
| | - Sofia Kiriakidi
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
- Departamento de Quimica Orgánica, Facultade de Quimica, Universidade de Vigo, 36310 Vigo, Spain
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (N.G.); (E.A.R.); (E.P.); (N.S.); (N.Z.); (K.M.); (S.K.)
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7
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Xia S, Chen E, Zhang Y. Integrated Molecular Modeling and Machine Learning for Drug Design. J Chem Theory Comput 2023; 19:7478-7495. [PMID: 37883810 PMCID: PMC10653122 DOI: 10.1021/acs.jctc.3c00814] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Modern therapeutic development often involves several stages that are interconnected, and multiple iterations are usually required to bring a new drug to the market. Computational approaches have increasingly become an indispensable part of helping reduce the time and cost of the research and development of new drugs. In this Perspective, we summarize our recent efforts on integrating molecular modeling and machine learning to develop computational tools for modulator design, including a pocket-guided rational design approach based on AlphaSpace to target protein-protein interactions, delta machine learning scoring functions for protein-ligand docking as well as virtual screening, and state-of-the-art deep learning models to predict calculated and experimental molecular properties based on molecular mechanics optimized geometries. Meanwhile, we discuss remaining challenges and promising directions for further development and use a retrospective example of FDA approved kinase inhibitor Erlotinib to demonstrate the use of these newly developed computational tools.
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Affiliation(s)
- Song Xia
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Eric Chen
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Simons
Center for Computational Physical Chemistry at New York University, New York, New York 10003, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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8
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Yetişsin F, Korkmaz A, Kaya E. In Silico and in Vitro Biological Evaluation of Novel Serial Sulfonate Derivatives on Pancreatic Lipase Activity. Chem Biodivers 2023; 20:e202301210. [PMID: 37743258 DOI: 10.1002/cbdv.202301210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 09/26/2023]
Abstract
The novel benzothiazole sulfonate hybrid derivatives containing azomethine group were synthesized and characterized using 1 H-NMR, 13 C-NMR, and HR-MS analysis. The potential enzyme inhibition activities against pancreatic lipase of the novel benzothiazole sulfonate hybrid derivatives containing azomethine group were screened with in vitro and in silico methods. IC50 values of compounds 5 b (23.89 μM), 5 i (28.87 μM), and 5 f (30.13±4.32) were found to be more effective pancreatic lipase inhibitors than orlistat (57.75 μM) in vitro studies. Also, the binding affinities of compounds 5 b (-8.7 kcal/mol), 5 i (-8.6 kcal/mol), and 5 f (-8.9 kcal/mol) were found potential inhibitors for pancreatic lipase in silico studies. In addition, the absorption distribution, metabolism, and excretion properties (ADME), molecular properties, toxicity estimation, and bioactivity scores of the synthesized compounds were scanned. It was found to have the ability to cross the brain-blood barrier for compounds 5 a, 5 b, 5 c, and 5 d. All compounds were calculated to be taken orally as drugs, suitable for absorption in the intestinal tract and not carcinogenic, as well as very strongly bound to plasma proteins. Finally, compound 5 f was observed to be the best inhibitor for pancreatic lipase according to in vitro and in silico studies.
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Affiliation(s)
- Fuat Yetişsin
- Muş Alparslan University, Technical Sciences Vocational School, 49250, Muş, Turkey
| | - Adem Korkmaz
- Faculty of Health Sciences, Muş Alparslan University, 49250, Muş, Turkey
| | - Esin Kaya
- Faculty of Education, Muş Alparslan University, Muş, 49250, Turkey
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9
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Korkmaz A, Kurtay G, Kaya E, Bursal E. Design, synthesis, spectroscopic characterizations, in vitro pancreatic lipase as well as tyrosinase inhibition evaluations and in silico analysis of novel aryl sulfonate-naphthalene hybrids. J Biomol Struct Dyn 2023; 41:7128-7143. [PMID: 36069113 DOI: 10.1080/07391102.2022.2116600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/18/2022] [Indexed: 10/14/2022]
Abstract
One of the primary purposes of this study is to synthesize new aryl sulfonate-naphthalene hybrid structures possessing divergent electron-withdrawing and electron-releasing functional groups. Following the improved reaction conditions, we successfully gathered ten distinct sulfonate derivatives (3a-j) with good yields. The synthesized naphthalene-based sulfonate derivatives were then characterized using appropriate analytical methods (FT-IR, 1H-NMR, 13C-NMR, HRMS, and elemental analysis). Additionally, in vitro and in silico enzyme inhibitory properties of the prepared aryl sulfonate-naphthalene hybrid structures were evaluated against pancreatic lipase and tyrosinase enzymes. Corresponding in vitro enzyme activity investigations revealed that the produced compounds inhibit pancreatic lipase and tyrosinase enzymes significantly. According to the lowest IC50 values, 3h (95.3 ± 4.0 µM) demonstrated the most effective inhibition against pancreatic lipase, whereas 3a (40.8 ± 3.3 µM) was found as the most effective inhibition against the tyrosinase. According to in silico studies, 3a exhibited the highest affinity value (-9.9 kcal/mol) against pancreatic lipase, whereas 3f demonstrated the best affinity value (-8.7 kcal/mol) against tyrosinase.Furthermore, we investigated various structural and physicochemical properties of the target molecules, namely frontier orbital' (HOMO, LUMO, and bandgap) energies (including their corresponding contour plots), global reactivity descriptors (ionization energy and electron affinity), and electronegativity values gathered from ground-state (GS) density functional theory (DFT) calculations. These investigations demonstrated that the observed electrostatic interactions effectively contributed to the studied molecules' experimentally demonstrated enzyme inhibition potential. Also, ADMET studies were evaluated to enlighten the molecular interactions of the compounds with the enzymes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adem Korkmaz
- Faculty of Health Sciences, Muş Alparslan University, Muş, Turkey
| | - Gülbin Kurtay
- Department of Chemistry, Faculty of Science, Ankara University, Ankara, Turkey
| | - Esin Kaya
- Faculty of Education, Muş Alparslan University, Muş, Turkey
| | - Ercan Bursal
- Faculty of Health Sciences, Muş Alparslan University, Muş, Turkey
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10
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Liu W, Li E, Liu L, Tian F, Luo X, Cai Y, Wang J, Jin X. Antifungal activity of compounds from Gordonia sp. WA8-44 isolated from the gut of Periplaneta americana and molecular docking studies. Heliyon 2023; 9:e17777. [PMID: 37539250 PMCID: PMC10395128 DOI: 10.1016/j.heliyon.2023.e17777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023] Open
Abstract
Invasive fungal infections are on the rise, leading to a continuous demand for antifungal antibiotics. Rare actinomycetes have been shown to contain a variety of interesting compounds worth exploring. In this study, 15 strains of rare actinobacterium Gordonia were isolated from the gut of Periplaneta americana and screened for their anti-fungal activity against four human pathogenic fungi. Strain WA8-44 was found to exhibit significant anti-fungal activity and was selected for bioactive compound production, separation, purification, and characterization. Three anti-fungal compounds, Collismycin A, Actinomycin D, and Actinomycin X2, were isolated from the fermentation broth of Gordonia strain WA8-44. Of these, Collismycin A was isolated and purified from the secondary metabolites of Gordonia for the first time, and its anti-filamentous fungi activity was firstly identified in this study. Molecular docking was carried out to determine their hypothetical binding affinities against nine target proteins of Candida albicans. Chitin Synthase 2 was found to be the most preferred antimicrobial protein target for Collismycin A, while 1,3-Beta-Glucanase was the most preferred anti-fungal protein target for Actinomycin D and Actinomycin X2. ADMET prediction revealed that Collismycin A has favorable oral bioavailability and little toxicity, making it a potential candidate for development as an orally active medication.
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Affiliation(s)
- Wenbin Liu
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Ertong Li
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Lingyan Liu
- School of Pharmacy, Xi'an Medical College, Xi'an 710300, PR China
| | - Fangyuan Tian
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Xiongming Luo
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yanqu Cai
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Xiaobao Jin
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
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11
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Azad I, Khan T, Ahmad N, Khan AR, Akhter Y. Updates on drug designing approach through computational strategies: a review. Future Sci OA 2023; 9:FSO862. [PMID: 37180609 PMCID: PMC10167725 DOI: 10.2144/fsoa-2022-0085] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/16/2023] Open
Abstract
The drug discovery and development (DDD) process in pursuit of novel drug candidates is a challenging procedure requiring lots of time and resources. Therefore, computer-aided drug design (CADD) methodologies are used extensively to promote proficiency in drug development in a systematic and time-effective manner. The point in reference is SARS-CoV-2 which has emerged as a global pandemic. In the absence of any confirmed drug moiety to treat the infection, the science fraternity adopted hit and trial methods to come up with a lead drug compound. This article is an overview of the virtual methodologies, which assist in finding novel hits and help in the progression of drug development in a short period with a specific medicinal solution.
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Affiliation(s)
- Iqbal Azad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Tahmeena Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Naseem Ahmad
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, P.O. Bas-ha, Kursi Road, Lucknow, 226026, UP, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, UP, 2260025, India
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12
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Georgiou N, Chontzopoulou E, Cheilari A, Katsogiannou A, Karta D, Vavougyiou K, Hadjipavlou-Litina D, Javornik U, Plavec J, Tzeli D, Vassiliou S, Mavromoustakos T. Thiocarbohydrazone and Chalcone-Derived 3,4-Dihydropyrimidinethione as Lipid Peroxidation and Soybean Lipoxygenase Inhibitors. ACS OMEGA 2023; 8:11966-11977. [PMID: 37033811 PMCID: PMC10077549 DOI: 10.1021/acsomega.2c07625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
The potential of the 4,6-diphenyl-3,4-dihydropyrimidine-2(1H)-thione (abbreviated as KKII5) and (E)-N'-benzylidenehydrazinecarbothiohydrazide (abbreviated as DKI5) compounds as possible drug leads is investigated. KKII5 and DKI5 are synthesized in high yield of up to 97%. Their structure, binding in the active site of the LOX-1 enzyme, and their toxicity are studied via joint experimental and computational methodologies. Specifically, the structure assignment and conformational analysis were achieved by applying homonuclear and heteronuclear 2D nuclear magnetic resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and density functional theory (DFT). The obtained DFT lowest energy conformers were in agreement with the NOE correlations observed in the 2D-NOESY spectra. Additionally, docking and molecular dynamics simulations were performed to discover their ability to bind and remain stabile in the active site of the LOX-1 enzyme. These in silico experiments and DFT calculations indicated favorable binding for the enzyme under study. The strongest binding energy, -9.60 kcal/mol, was observed for dihydropyrimidinethione KKII5 in the active site of LOX-1. ADMET calculations showed that the two molecules lack major toxicities and could serve as possible drug leads. The redox potential of the active center of LOX-1 with the binding molecules was calculated via DFT methodology. The results showed a significantly smaller energy attachment of 2.8 eV with KKII5 binding in comparison to DKI5. Thus, KKII5 enhanced the ability of the active center to receive electrons compared to DKI5. This is related to the stronger binding interaction of KKII5 relative to that of DK15 to LOX-1. The two very potent LOX-1 inhibitors exerted IC50 19 μΜ (KKII5) and 22.5 μΜ (DKI5). Furthermore, they both strongly inhibit lipid peroxidation, namely, 98% for KKII5 and 94% for DKI5.
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Affiliation(s)
- Nikitas Georgiou
- Laboratory
of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
| | - Eleni Chontzopoulou
- Laboratory
of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
| | - Antigoni Cheilari
- Department
of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece
| | - Aikaterini Katsogiannou
- Laboratory
of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
| | - Danai Karta
- Laboratory
of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
| | - Kyriaki Vavougyiou
- Laboratory
of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
| | - Dimitra Hadjipavlou-Litina
- Department
of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health
Sciences,, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Uroš Javornik
- Slovenian
NMR Centre, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian
NMR Centre, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | - Demeter Tzeli
- Laboratory
of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
- Theoretical
and Physical Chemistry Institute, National
Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Stamatia Vassiliou
- Laboratory
of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
| | - Thomas Mavromoustakos
- Laboratory
of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 11571 Athens, Greece
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13
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Laskar YB, Mazumder PB, Talukdar AD. Hibiscus sabdariffa anthocyanins are potential modulators of estrogen receptor alpha activity with favourable toxicology: a computational analysis using molecular docking, ADME/Tox prediction, 2D/3D QSAR and molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:611-633. [PMID: 34854367 DOI: 10.1080/07391102.2021.2009914] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The estrogen hormone receptor (ER) mediated gene expression mainly regulate the development and physiology of the primary and secondary reproductive system alongside bone-forming, metabolism and behaviour. Over-expressed ER is associated with several pathological conditions and play a crucial role in breast cancer occurrence, progression and metastasis. Hibiscus sabdariffa L. or roselle is a rich source of naturally occurring polyphenolic compounds that reportedly have robust estrogenic activity. However, the estrogen-like ingredient of the plant remains ambiguous. This study has screened a library of already recorded and less-explored compounds of Hibiscus sabdariffa for their estrogen receptor binding affinity and safety using a suite of computational methods that include protein-ligand docking, ADME and Toxicity prediction, and 2D/3D QSAR. The study revealed that the estrogen-receptor binding potential of Pelargonidin, Delphinidin, Cyanidin, and Hibiscetin are more efficient than popular breast cancer drugs, Tamoxifen and Raloxifene. Besides, the compounds exhibited favourable toxicological parameters with potent bioactivity towards binding ER-α subunit. Thus, these compounds can serve as prototypes for designing novel Selective Estrogen Receptor Modulator molecules with a few structural modifications. This is the first report exploring the phytochemical basis of estrogenic activity of Hibiscus sabdariffa L.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yahyea Baktiar Laskar
- Natural Product and Biomedicine Research Laboratory, Department of Biotechnology, Assam University, Silchar, India
| | - Pranab Behari Mazumder
- Natural Product and Biomedicine Research Laboratory, Department of Biotechnology, Assam University, Silchar, India
| | - Anupam Das Talukdar
- Ethnobotany and Medicinal Plants Research Laboratory, Department of Life Science & Bioinformatics, Assam University, Silchar, India
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14
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Analyzing Indole-fused benzooxazepines as inhibitors of apoptosis pathway-related proteins using multifaceted computational medicinal chemistry. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Swetha R, Sharma A, Singh R, Ganeshpurkar A, Kumar D, Kumar A, Singh SK. Combined ligand-based and structure-based design of PDE 9A inhibitors against Alzheimer's disease. Mol Divers 2022; 26:2877-2892. [PMID: 35932437 DOI: 10.1007/s11030-022-10504-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/22/2022] [Indexed: 10/16/2022]
Abstract
PDE9 enzyme hydrolyzes cGMP, which is involved in the regulation of synaptic plasticity through the NMDA pathway (a well-known excitotoxic target for AD) via activation of calcium/calmodulin-dependent neuronal NO synthases in the postsynaptic neurons. The inhibition of PDE9 leads to elevated cGMP levels, causing enhanced NMDA signaling and thus contributing to an increase in synaptic plasticity and stabilization. Therefore, it could be considered a pertinent target for AD drug discovery. PF-04447943 and BI-409306 targeting PDE9 are undergoing clinical trials (Phase II). The present study encompasses a pharmacophoric approach to identify potent PDE9 inhibitors using various computational methods. Pharmacophores generated from the PDB 6A3N yielded 37,554 virtual hits, which underwent drug likeliness and PAINS filtering to arrive at a few virtual leads. The leads were further subjected to extra precision docking, ADMET predictions, and molecular dynamics. The final hits, ZINC000001305675 and ZINC000000377099, showed superior docking scores of - 10.90 and - 10.30 kcal/mol and satisfactory predicted ADMET scores. The hits were subjected to molecular dynamics (MD) studies, wherein they formed stable complexes with PDE9 protein and had ligand RMSDs within acceptable limits. The processes involved in the combined ligand and structure-based strategies.
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Affiliation(s)
- Rayala Swetha
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Anjali Sharma
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ankit Ganeshpurkar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharti Vidyapeeth University, Pune, India
| | | | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Sushil K Singh
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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16
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Insight into the Crystal Structures and Potential of Two Newly Synthesized Naproxen-Based Hydrazide Derivatives as Potent COX-2 Inhibitors. Appl Biochem Biotechnol 2022; 194:5781-5807. [PMID: 35819690 DOI: 10.1007/s12010-022-04077-2] [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: 04/28/2022] [Accepted: 07/05/2022] [Indexed: 11/02/2022]
Abstract
Although nonsteroidal anti-inflammatory drugs (NSAIDs) are medicines that are widely used to relieve pain, reduce inflammation, and bring down high temperature, literature confirmed that they still have harmful side effects. Most of their side effects are in the digestive system due to the carboxylic group. As naproxen is one of the NSAIDs, in this work, we try to mask the carboxylic group in naproxen with a relatively safe functional group. So, herein, we report the synthesis of new naproxen-based hydrazones derivatives, namely, (E)-N'-1-(4-chlorophenyl)ethylidene)-2-(6-methoxynaphthalen-2-yl)propane hydrazide (4a) and (E)-N'-(4-hydroxybenzylidene)-2-(6-methoxynaphthalen-2-yl)propane hydrazide ethanol solvate (4b). The compounds were confirmed by X-ray diffraction studies. Hirshfeld surface analyses and energy frameworks of 4a and 4b have been carried out and blind molecular docking studies of them to the COX-2 enzyme were undertaken to obtain binding affinities for judging whether the compounds could act as anti-inflammatory agents. The compounds interact with the key residues: Arg120, Val349, Leu352, Tyr355, Val523, Ala527, Ser530, and Leu531 of the active enzyme pocket. Molecular dynamics studies predicted that the complexes of 4a and 4b with COX-2 are structurally stable and no major conformational changes were observed. Confirmation of the docking and simulation data was achieved by a binding free energies analysis that indicated the dominance of van der Waals energy. The compounds are drug-like molecules as they obey all prominent drug-like rules and have acceptable pharmacokinetic profiles. To investigate the relationship between their intrinsic electronic properties and their possible similarities to actual drugs, the gas-phase DFT optimizations and NBO analyses were also performed in this study.
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17
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Hasan MR, Alsaiari AA, Fakhurji BZ, Molla MHR, Asseri AH, Sumon MAA, Park MN, Ahammad F, Kim B. Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process. Molecules 2022; 27:4169. [PMID: 35807415 PMCID: PMC9268380 DOI: 10.3390/molecules27134169] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 01/18/2023] Open
Abstract
The conventional drug discovery approach is an expensive and time-consuming process, but its limitations have been overcome with the help of mathematical modeling and computational drug design approaches. Previously, finding a small molecular candidate as a drug against a disease was very costly and required a long time to screen a compound against a specific target. The development of novel targets and small molecular candidates against different diseases including emerging and reemerging diseases remains a major concern and necessitates the development of novel therapeutic targets as well as drug candidates as early as possible. In this regard, computational and mathematical modeling approaches for drug development are advantageous due to their fastest predictive ability and cost-effectiveness features. Computer-aided drug design (CADD) techniques utilize different computer programs as well as mathematics formulas to comprehend the interaction of a target and drugs. Traditional methods to determine small-molecule candidates as a drug have several limitations, but CADD utilizes novel methods that require little time and accurately predict a compound against a specific disease with minimal cost. Therefore, this review aims to provide a brief insight into the mathematical modeling and computational approaches for identifying a novel target and small molecular candidates for curing a specific disease. The comprehensive review mainly focuses on biological target prediction, structure-based and ligand-based drug design methods, molecular docking, virtual screening, pharmacophore modeling, quantitative structure-activity relationship (QSAR) models, molecular dynamics simulation, and MM-GBSA/MM-PBSA approaches along with valuable database resources and tools for identifying novel targets and therapeutics against a disease. This review will help researchers in a way that may open the road for the development of effective drugs and preventative measures against a disease in the future as early as possible.
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Affiliation(s)
- Md Rifat Hasan
- Department of Mathematics, Faculty of Science, King Abdul-Aziz University, Jeddah 21589, Saudi Arabia;
- Department of Applied Mathematics, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ahad Amer Alsaiari
- College of Applied Medical Science, Clinical Laboratories Science Department, Taif University, Taif 21944, Saudi Arabia;
| | - Burhan Zain Fakhurji
- iGene Medical Training and Molecular Research Center, Jeddah 21589, Saudi Arabia;
| | | | - Amer H. Asseri
- Biochemistry Department, Faculty of Science, King Abdul-Aziz University, Jeddah 21589, Saudi Arabia;
- Centre for Artificial Intelligence in Precision Medicines, King Abdul-Aziz University, Jeddah 21589, Saudi Arabia
| | - Md Afsar Ahmed Sumon
- Department of Marine Biology, Faculty of Marine Sciences, King Abdul-Aziz University, Jeddah 21589, Saudi Arabia;
| | - Moon Nyeo Park
- College of Korean Medicine, Kyung Hee University, Hoigidong, Dongdaemungu, Seoul 02453, Korea;
| | - Foysal Ahammad
- Department of Biological Sciences, Faculty of Science, King Abdul-Aziz University, Jeddah 21589, Saudi Arabia;
| | - Bonglee Kim
- College of Korean Medicine, Kyung Hee University, Hoigidong, Dongdaemungu, Seoul 02453, Korea;
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18
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Conformational Properties of New Thiosemicarbazone and Thiocarbohydrazone Derivatives and Their Possible Targets. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082537. [PMID: 35458736 PMCID: PMC9028911 DOI: 10.3390/molecules27082537] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022]
Abstract
The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydrazone KKI18 were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations using Functional Density Theory (DFT). After the structure identification of the compounds, various conformations of the two compounds were calculated using DFT. The two molecules showed the most energy-favorable values when their two double bonds adopted the E configuration. These configurations were compatible with the spatial correlations observed in the 2D-NOESY spectrum. In addition, due to the various isomers that occurred, the energy of the transition states from one isomer to another was calculated. Finally, molecular binding experiments were performed to detect potential targets for KKI15 and KKI18 derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for all four enzymes studied. The strongest binding energy was observed in the enzyme butyrylcholinesterase. ADMET calculations using the preADMET and pKCSm software showed that the two molecules appear as possible drug leads.
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19
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Paul A, Limon BH, Hossain M, Raza T. An integrated computational approach to screening of alkaloids inhibitors of TBX3 in breast cancer cell lines. J Biomol Struct Dyn 2022; 41:3025-3041. [PMID: 35253621 DOI: 10.1080/07391102.2022.2046166] [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
TBX3 is an ancient and evolutionarily conserved family member of T-box transcription factors that acts as a key regulator in embryonic development and organogenesis. It is often overexpressed in various epithelial and mesenchymal malignancies which has a significant impact on various hallmarks of cancer, which mainly includes senescence shunt, apoptosis, anoikis, angiogenesis, and promoting metastatic and expansion of cancer stem cells. In addition to the role of TBX3 in early breast development, a number of studies have also confirmed the amplification of TBX3 in the occurrence and development of breast cancer. To overcome a major challenge in breast cancer treatment, resistance to current anti-cancer drug, it is important to develop new drug pipeline. In this study of different alkaloid molecules, to identify potential alkaloid inhibitors of TBX3, a structure based virtual screening was done involving molecular docking, ADME, toxicity analysis, molecular dynamics simulation. From our study 5 ligands named Jervine, Diflomotecan, Camptothecin, Vincamine, and Anoniane were primarily confirmed as potential inhibitors. The followed screening manner funnels out five potential compounds that have a high scoring function that emphasizes their high binding ability along with no toxicity effects. The molecular mechanics-generalized born surface area (MM-GBSA) and molecular dynamics (MD) simulation showed that Jervine along with Diflomotecan formed the stable complexes with TBX3 which makes it obvious that these two alkaloids can be introduced into the drug development pipeline and used as a new leader to develop new effective drugs against breast cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anjasu Paul
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | | | - Mobarok Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Thosif Raza
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
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20
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Batista MA, de Lima Teixeira dos Santos AVT, do Nascimento AL, Moreira LF, Souza IRS, da Silva HR, Pereira ACM, da Silva Hage-Melim LI, Carvalho JCT. Potential of the Compounds from Bixa orellana Purified Annatto Oil and Its Granules (Chronic ®) against Dyslipidemia and Inflammatory Diseases: In Silico Studies with Geranylgeraniol and Tocotrienols. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27051584. [PMID: 35268686 PMCID: PMC8911567 DOI: 10.3390/molecules27051584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022]
Abstract
Some significant compounds present in annatto are geranylgeraniol and tocotrienols. These compounds have beneficial effects against hyperlipidemia and chronic diseases, where oxidative stress and inflammation are present, but the exact mechanism of action of such activities is still a subject of research. This study aimed to evaluate possible mechanisms of action that could be underlying the activities of these molecules. For this, in silico approaches such as ligand topology (PASS and SEA servers) and molecular docking with the software GOLD were used. Additionally, we screened some pharmacokinetic and toxicological parameters using the servers PreADMET, SwissADME, and ProTox-II. The results corroborate the antidyslipidemia and anti-inflammatory activities of geranylgeraniol and tocotrienols. Notably, some new mechanisms of action were predicted to be potentially underlying the activities of these compounds, including inhibition of squalene monooxygenase, lanosterol synthase, and phospholipase A2. These results give new insight into new mechanisms of action involved in these molecules from annatto and Chronic®.
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Affiliation(s)
- Mateus Alves Batista
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Amapá, Macapá 68902-280, Brazil; (M.A.B.); (L.I.d.S.H.-M.)
| | - Abrahão Victor Tavares de Lima Teixeira dos Santos
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, km 02, Amapá, Macapá 68902-280, Brazil; (A.V.T.d.L.T.d.S.); (A.L.d.N.); (L.F.M.); (H.R.d.S.)
| | - Aline Lopes do Nascimento
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, km 02, Amapá, Macapá 68902-280, Brazil; (A.V.T.d.L.T.d.S.); (A.L.d.N.); (L.F.M.); (H.R.d.S.)
| | - Luiz Fernando Moreira
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, km 02, Amapá, Macapá 68902-280, Brazil; (A.V.T.d.L.T.d.S.); (A.L.d.N.); (L.F.M.); (H.R.d.S.)
| | - Indira Ramos Senna Souza
- Diamantina Chapada Regional Hospital, Avenida Francisco Costa, 350-468, Vasco Filho, Bahia, Seabra 46900-000, Brazil;
| | - Heitor Ribeiro da Silva
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, km 02, Amapá, Macapá 68902-280, Brazil; (A.V.T.d.L.T.d.S.); (A.L.d.N.); (L.F.M.); (H.R.d.S.)
| | - Arlindo César Matias Pereira
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), São Paulo, Ribeirão Preto 05508-000, Brazil;
| | - Lorane Izabel da Silva Hage-Melim
- Laboratory of Pharmaceutical and Medicinal Chemistry (PharMedChem), Federal University of Amapá, Amapá, Macapá 68902-280, Brazil; (M.A.B.); (L.I.d.S.H.-M.)
| | - José Carlos Tavares Carvalho
- Laboratory of Drugs Research, Biology and Healthy Sciences Department, Pharmacy Faculty, Federal University of Amapá, Rod. JK, km 02, Amapá, Macapá 68902-280, Brazil; (A.V.T.d.L.T.d.S.); (A.L.d.N.); (L.F.M.); (H.R.d.S.)
- Correspondence:
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21
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Amide-based xanthine oxidase inhibitors bearing an N-(1-alkyl-3-cyano-1H-indol-5-yl) moiety: Design, synthesis and structure-activity relationship investigation. Bioorg Chem 2021; 117:105417. [PMID: 34673452 DOI: 10.1016/j.bioorg.2021.105417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/21/2021] [Accepted: 10/06/2021] [Indexed: 12/29/2022]
Abstract
Our previous work identified a promising isonicotinamide based xanthine oxidase (XO) inhibitor, N-(3-cyano-4-((2-cyanobenzyl)oxy)phenyl)isonicotinamide (1), and concluded that amide is an effective linker in exploring the XO inhibitor chemical space that is completely different from the five-membered ring framework of febuxostat and topiroxostat. Indole, an endogenous bioactive substance and a popular drug construction fragment, was involved in the structural optimization campaign of the present effort. After the installation of some functional groups, N-(1-alkyl-3-cyano-1H-indol-5-yl) was generated and employed to mend the missing H-bond interaction between the 3'-cyano of 1 and Asn768 residue of XO by shortening their distance. In this context, eight kinds of heterocyclic aromatic amide chemotypes were rationally designed and synthesized to investigate the structure-activity relationship (SAR) of amide-based XO inhibitors. The optimized compound a6 (IC50 = 0.018 μM) exhibits 17.2-fold improved potency than the initial compound 1 (IC50 = 0.31 μM). Its potency is comparable to that of topiroxostat (IC50 = 0.013 μM). Molecular docking and molecular dynamics studies proved the existence of the stable H-bond between the cyano group and the Asn768 residue. Moreover, oral administration of a6 (11.8 mg/kg) could effectively reduce serum uric acid levels in an acute hyperuricemia rat model. Liver microsomal stability assay illustrated that compound a6 possesses well metabolic stability in rat liver microsomes. However, the in vivo potency of a6 was much lower than that of topiroxostat, which may be explained by the poor absorption found in the parallel artificial membrane permeability assay (PAMPA). In addition, 6a has non-cytotoxicity against normal cell lines MCF10A and 16HBE. Taken together, this work culminated in the identification of compound 6a as an excellent lead for further exploration of amide-based XO inhibitors.
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Shaker B, Ahmad S, Lee J, Jung C, Na D. In silico methods and tools for drug discovery. Comput Biol Med 2021; 137:104851. [PMID: 34520990 DOI: 10.1016/j.compbiomed.2021.104851] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/05/2021] [Accepted: 09/05/2021] [Indexed: 12/28/2022]
Abstract
In the past, conventional drug discovery strategies have been successfully employed to develop new drugs, but the process from lead identification to clinical trials takes more than 12 years and costs approximately $1.8 billion USD on average. Recently, in silico approaches have been attracting considerable interest because of their potential to accelerate drug discovery in terms of time, labor, and costs. Many new drug compounds have been successfully developed using computational methods. In this review, we briefly introduce computational drug discovery strategies and outline up-to-date tools to perform the strategies as well as available knowledge bases for those who develop their own computational models. Finally, we introduce successful examples of anti-bacterial, anti-viral, and anti-cancer drug discoveries that were made using computational methods.
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Affiliation(s)
- Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Jingyu Lee
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Chanjin Jung
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
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Valéria Amorim L, de Lima Moreira D, Muálem de Moraes Alves M, Jessé Ramos Y, Pereira Costa Sobrinho E, Arcanjo DDR, Rodrigues de Araújo A, de Souza de Almeida Leite JR, das Chagas Pereira de Andrade F, Mendes AN, Aécio de Amorim Carvalho F. Anti-Leishmania activity of extracts from Piper cabralanum C.DC. (Piperaceae). ACTA ACUST UNITED AC 2021; 76:229-241. [PMID: 33660490 DOI: 10.1515/znc-2020-0284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/06/2021] [Indexed: 11/15/2022]
Abstract
Species of Piperaceae are known by biological properties, including antiparasitic such as leishmanicidal, antimalarial and in the treatment of schistosomiasis. The aim of this work was to evaluate the antileishmania activity, cytotoxic effect, and macrophage activation patterns of the methanol (MeOH), hexane (HEX), dichloromethane (DCM) and ethyl acetate (EtOAc) extract fractions from the leaves of Piper cabralanum C.DC. The MeOH, HEX and DCM fractions inhibited Leishmanina amazonensis promastigote-like forms growth with a half maximal inhibitory concentration (IC50) of 144.54, 59.92, and 64.87 μg/mL, respectively. The EtOAc fraction did not show any relevant activity. The half maximal cytotoxic concentration (CC50) for macrophages were determined as 370.70, 83.99, 113.68 and 607 μg/mL for the MeOH, HEX and DCM fractions, respectively. The macrophage infectivity was concentration-dependent, especially for HEX and DCM. MeOH, HEX and DCM fractions showed activity against L. amazonensis with low cytotoxicity to murine macrophages and lowering infectivity by the parasite. Our results provide support for in vivo studies related to a potential application of P. cabralanum extract and fractions as a promising natural resource in the treatment of leishmaniasis.
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Affiliation(s)
- Layane Valéria Amorim
- Antileishmania Activity Laboratory, Federal University of Piauí, Teresina, Piauí, Brazil
| | - Davyson de Lima Moreira
- Natural Products Laboratory, Institute of Pharmaceutical Tecnologies, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro-RJ, Brazil
| | | | - Ygor Jessé Ramos
- Natural Products Laboratory, Institute of Pharmaceutical Tecnologies, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro-RJ, Brazil
| | | | - Daniel Dias Rufino Arcanjo
- Department of Biophysics and Physiology, Laboratory of Funcional and Molecular Studies in Physiopharmacology, Federal University of Piauí, Teresina, Piauí, Brazil
| | - Alyne Rodrigues de Araújo
- Research Center on Biodiversity and Biotechnology, BIOTEC, Federal University of Delta of Parnaíba, UFDPar, Parnaíba, Piauí, Brazil
| | | | | | - Anderson Nogueira Mendes
- Department of Biophysics and Physiology, Laboratory of Innovation on Science and Technology, Federal University of Piauí, Teresina, Piauí, Brazil
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Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight. Molecules 2021; 26:molecules26041079. [PMID: 33670773 PMCID: PMC7922218 DOI: 10.3390/molecules26041079] [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: 01/22/2021] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA–FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.
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