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Dhivya LS, Manoharadas S, Pandiaraj S, Thiruvengadam M, Viswanathan D, Govindasamy R. Halogenated chalcones against Mycobacterium tuberculosis targeting InhA: Rational design, in silico and in vitro evaluation. Microb Pathog 2024; 196:106945. [PMID: 39284520 DOI: 10.1016/j.micpath.2024.106945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/10/2024] [Accepted: 09/13/2024] [Indexed: 09/21/2024]
Abstract
A library of 25-series compounds was designed against Mycobacterium Tuberculosis (M.tb) to identify novel antitubercular drugs. In silico inhibition of InhA, an essential component of FAS-II, was successfully achieved. The drug ability, lead-likeness, and toxicity of the compounds were assessed using Swiss ADME, pkCSM, and Osiris Property Explorer, which revealed the potential for drug development of chalcone compounds. Through in silico research, it was confirmed that toxic-free compounds could bind to InhA. It was found that all of the compounds bind to InhA with binding affinities ranging from -7.78 to -10.29 kcal/mol-1 which is higher than the reference standard Isoniazid and Pyrazinamide. The top five compounds were synthesized from 15 toxic-free compounds. The structural characteristics of the compounds were determined using IR, NMR, and mass spectrometry techniques. These findings indicate that these substances are competitive, reversible, and specific InhA inhibitors of InhA. using the Alamar Blue assay method (H37RV, ATCC No. 27294), the in vitro anti-mycobacterial activity of each of the synthesized compounds against M.tb was evaluated. The two most powerful compounds were (2E)-3-[4-(benzyloxy)-3,5-dimethylphenyl] and (2E)-1-(3,5-dibromophenyl)-3-(3-phenoxyphenyl) prop-2-en-1-one. In the MABA Assay, the MIC for 1-(3,5-dibromophenyl) prop-2-en-1-one was 6.25 μg/ml.
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Affiliation(s)
- L S Dhivya
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Dr MGR Educational and Research Institute, Velappanchavadi, Chennai, 77, Tamil Nadu, India
| | - Salim Manoharadas
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2454, Riyadh, Saudi Arabia
| | - Saravanan Pandiaraj
- Department of Self-Development Skills, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, 05029, South Korea
| | - Dhivya Viswanathan
- Department of Orthodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, Tamilnadu, India
| | - Rajakumar Govindasamy
- Department of Orthodontics, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600077, Tamilnadu, India.
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Vaziri-Amjad S, Rahgosha R, Taherkhani A. Potential JAK2 Inhibitors from Selected Natural Compounds: A Promising Approach for Complementary Therapy in Cancer Patients. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2024; 2024:1114928. [PMID: 38706884 PMCID: PMC11068457 DOI: 10.1155/2024/1114928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 02/14/2024] [Accepted: 04/02/2024] [Indexed: 05/07/2024]
Abstract
Background Janus-activated kinase 2 (JAK2) plays a pivotal role in numerous essential biological processes, including proliferation, apoptosis, and metastasis in human cells. Prior studies have indicated that inhibiting JAK2 could be a promising strategy to mitigate cell proliferation and induce apoptosis in tumor cells. Objectives This study aimed to estimate the binding affinity of 79 herbal compounds, comprising 46 flavonoids, 21 anthraquinones, and 12 cinnamic acids, to the ATP-binding cleft of JAK2 to identify potential herbal inhibitors of JAK2. Methods The binding affinities between ligands and JAK2 were calculated utilizing AutoDock 4.0 software in conjunction with the Cygwin environment. Cross-validation was conducted using the Schrödinger tool. Molecular dynamics simulations were employed to evaluate the stability of docked poses for the most significant JAK2 inhibitors. Furthermore, the Discovery Studio Visualizer tool was utilized to elucidate interactions between the top-ranked JAK2 inhibitors and residues within the JAK2 ATP-binding site. Results Twelve flavonoids, two anthraquinones, and three cinnamic acids demonstrated substantial binding affinities to the protein kinase domain of the receptor, with a criterion of ΔGbinding < -10 kcal/mol. Among the studied flavonoids, anthraquinones, and cinnamic acid derivatives, orientin, chlorogenic acid, and pulmatin emerged as the most potent JAK2 inhibitors, exhibiting ΔGbinding scores of -14.49, -11.87, and -10.76 kcal/mol, respectively. Furthermore, the docked poses of orientin, pulmatin, and chlorogenic acid remained stable throughout 60 ns computer simulations. The average root mean square deviation values calculated for JAK2 when complexed with orientin, chlorogenic acid, and pulmatin were 2.04 Å, 2.06 Å, and 1.95 Å, respectively. Conclusion This study underscores the robust inhibitory potential of orientin, pulmatin, and chlorogenic acid against JAK2. The findings hold promise for the development of novel and effective drugs for cancer treatment.
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Affiliation(s)
- Samaneh Vaziri-Amjad
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Reza Rahgosha
- Department of Oral and Maxillofacial Medicine, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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Tarbeeva DV, Pislyagin EA, Menchinskaya ES, Berdyshev DV, Krylova NV, Iunikhina OV, Kalinovskiy AI, Shchelkanov MY, Mishchenko NP, Aminin DL, Fedoreyev SA. Polyphenols from Maackia amurensis Heartwood Protect Neuronal Cells from Oxidative Stress and Prevent Herpetic Infection. Int J Mol Sci 2024; 25:4142. [PMID: 38673729 PMCID: PMC11050087 DOI: 10.3390/ijms25084142] [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: 03/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Here, we continued the investigation of anti-HSV-1 activity and neuroprotective potential of 14 polyphenolic compounds isolated from Maackia amurensis heartwood. We determined the absolute configurations of asymmetric centers in scirpusin A (13) and maackiazin (10) as 7R,8R and 1″S,2″S, respectively. We showed that dimeric stilbens maackin (9) and scirpusin A (13) possessed the highest anti-HSV-1 activity among polyphenols 1-14. We also studied the effect of polyphenols 9 and 13 on the early stages of HSV-1 infection. Direct interaction with the virus (virucidal activity) was the main mechanism of the antiviral activity of these compounds. The neuroprotective potential of polyphenolic compounds from M. amurensis was studied using models of 6-hydroxydopamine (6-OHDA)-and paraquat (PQ)-induced neurotoxicity. A dimeric stilbene scirpusin A (13) and a flavonoid liquiritigenin (6) were shown to be the most active compounds among the tested polyphenols. These compounds significantly increased the viability of 6-OHDA-and PQ-treated Neuro-2a cells, elevated mitochondrial membrane potential and reduced the intracellular ROS level. We also found that scirpusin A (13), liquiritigenin (6) and retusin (3) considerably increased the percentage of live Neuro-2a cells and decreased the number of early apoptotic cells. Scirpusin A (13) was the most promising compound possessing both anti-HSV-1 activity and neuroprotective potential.
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Affiliation(s)
- Darya V. Tarbeeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
| | - Evgeny A. Pislyagin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
| | - Ekaterina S. Menchinskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
| | - Dmitrii V. Berdyshev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
| | - Natalya V. Krylova
- G.P. Somov Institute of Epidemiology and Microbiology, Rospotrebnadzor, 690087 Vladivostok, Russia; (N.V.K.); (O.V.I.); (M.Y.S.)
| | - Olga V. Iunikhina
- G.P. Somov Institute of Epidemiology and Microbiology, Rospotrebnadzor, 690087 Vladivostok, Russia; (N.V.K.); (O.V.I.); (M.Y.S.)
| | - Anatoliy I. Kalinovskiy
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
| | - Mikhail Y. Shchelkanov
- G.P. Somov Institute of Epidemiology and Microbiology, Rospotrebnadzor, 690087 Vladivostok, Russia; (N.V.K.); (O.V.I.); (M.Y.S.)
| | - Natalia P. Mishchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
| | - Dmitry L. Aminin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
| | - Sergey A. Fedoreyev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia; (E.A.P.); (E.S.M.); (D.V.B.); (A.I.K.); (N.P.M.); (D.L.A.); (S.A.F.)
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Lian X, Fan K, Qin X, Liu Y. Amalgamated Pharmacoinformatics Study to Investigate the Mechanism of Xiao Jianzhong Tang against Chronic Atrophic Gastritis. Curr Comput Aided Drug Des 2024; 20:598-615. [PMID: 37475552 DOI: 10.2174/1573409919666230720141115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/24/2023] [Accepted: 06/14/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Traditional Chinese medicine (TCM) Xiao Jianzhong Tang (XJZ) has a favorable efficacy in the treatment of chronic atrophic gastritis (CAG). However, its pharmacological mechanism has not been fully explained. OBJECTIVE The purpose of this study was to find the potential mechanism of XJZ in the treatment of CAG using pharmacocoinformatics approaches. METHODS Network pharmacology was used to screen out the key compounds and key targets, MODELLER and GNNRefine were used to repair and refine proteins, Autodock vina was employed to perform molecular docking, Δ Lin_F9XGB was used to score the docking results, and Gromacs was used to perform molecular dynamics simulations (MD). RESULTS Kaempferol, licochalcone A, and naringenin, were obtained as key compounds, while AKT1, MAPK1, MAPK14, RELA, STAT1, and STAT3 were acquired as key targets. Among docking results, 12 complexes scored greater than five. They were run for 50ns MD. The free binding energy of AKT1-licochalcone A and MAPK1-licochalcone A was less than -15 kcal/mol and AKT1-naringenin and STAT3-licochalcone A was less than -9 kcal/mol. These complexes were crucial in XJZ treating CAG. CONCLUSION Our findings suggest that licochalcone A could act on AKT1, MAPK1, and STAT3, and naringenin could act on AKT1 to play the potential therapeutic effect on CAG. The work also provides a powerful approach to interpreting the complex mechanism of TCM through the amalgamation of network pharmacology, deep learning-based protein refinement, molecular docking, machine learning-based binding affinity estimation, MD simulations, and MM-PBSA-based estimation of binding free energy.
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Affiliation(s)
- Xu Lian
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
- Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
| | - Kaidi Fan
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
- Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
- Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
| | - Yuetao Liu
- Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
- Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, No. 92, Wucheng Road, Taiyuan, 030006, Shanxi, P.R. China
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Ibrahim MAA, Ali SSM, Abdeljawaad KAA, Abdelrahman AHM, Gabr GA, Shawky AM, Mekhemer GAH, Sidhom PA, Paré PW, Hegazy MEF. In-silico natural product database mining for novel neuropilin-1 inhibitors: molecular docking, molecular dynamics and binding energy computations. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2023. [DOI: 10.1080/16583655.2023.2182623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sara S. M. Ali
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Khlood A. A. Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Alaa H. M. Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Gamal A. Gabr
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center, Giza, Egypt
| | - Ahmed M. Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia
| | - Gamal A. H. Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Peter A. Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Paul W. Paré
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX, USA
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Afiadenyo M, Adams L, Agoni C, Moane S, Mckeon-Bennett M, Obiri-Yeboah D, Singh J. Computational Screening of Neuropilin-1 Unveils Novel Potential Anti-SARS-CoV-2 Therapeutics. Chem Biodivers 2023; 20:e202301227. [PMID: 37878727 DOI: 10.1002/cbdv.202301227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Neuropilin 1 (NRP-1) inhibition has shown promise in reducing the infectivity of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and preventing the virus entry into nerve tissues, thereby mitigating neurological symptoms in COVID-19 patients. In this study, we employed virtual screening, including molecular docking, Molecular Dynamics (MD) simulation, and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations, to identify potential NRP-1 inhibitors. From a compendium of 1930 drug-like natural compounds, we identified five potential leads: CNP0435132, CNP0435311, CNP0424372, CNP0429647, and CNP0427474, displaying robust binding energies of -8.2, -8.1, -10.7, -8.2, and -8.2 kcal/mol, respectively. These compounds demonstrated interactions with critical residues Tyr297, Trp301, Thr316, Asp320, Ser346, Thr349, and Tyr353 located within the b1 subdomain of NRP-1. Furthermore, MD simulations and MM-PBSA calculations affirmed the stability of the complexes formed, with average root mean square deviation, radius of gyration, and solvent accessible surface area values of 0.118 nm, 1.516 nm, and 88.667 nm2 , respectively. Notably, these lead compounds were estimated to penetrate the blood-brain barrier and displayed antiviral properties, with Pa values ranging from 0.414 to 0.779. The antagonistic effects of these lead compounds merit further investigation, as they hold the potential to serve as foundational scaffolds for the development of innovative therapeutics aimed at reducing the neuroinfectivity of SARS-CoV-2.
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Affiliation(s)
- Michael Afiadenyo
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Latif Adams
- Technological University of Shannon: Midlands Midwest Midlands Campus, Athlone, Ireland
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Clement Agoni
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Belfield D04, V1 W8, Ireland
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
- West African Centre for Computational Research and Innovation, Ghana
| | - Siobhan Moane
- Technological University of Shannon: Midlands Midwest Midlands Campus, Athlone, Ireland
| | | | - Dorcas Obiri-Yeboah
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Jasdeep Singh
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, Delhi, India
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Alom MM, Bonna RP, Islam A, Alom MW, Rahman ME, Faruqe MO, Khalekuzzaman M, Zaman R, Islam MA. Unveiling Neuroprotective Potential of Spice Plant-Derived Compounds against Alzheimer's Disease: Insights from Computational Studies. Int J Alzheimers Dis 2023; 2023:8877757. [PMID: 37744007 PMCID: PMC10516701 DOI: 10.1155/2023/8877757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/26/2023] [Accepted: 08/26/2023] [Indexed: 09/26/2023] Open
Abstract
Alzheimer's disease (AD) is a serious threat to the global health care system and is brought on by a series of factors that cause neuronal dysfunction and impairment in memory and cognitive decline. This study investigated the therapeutic potential of phytochemicals that belong to the ten regularly used spice plants, based on their binding affinity with AD-associated proteins. Comprehensive docking studies were performed using AutoDock Vina in PyRx followed by molecular dynamic (MD) simulations using AMBER 14. The docking study of the chosen molecules revealed the binding energies of their interactions with the target proteins, while MD simulations were carried out to verify the steadiness of bound complexes. Through the Lipinski filter and admetSAR analysis, the chosen compounds' pharmacokinetic characteristics and drug likeness were also examined. The pharmacophore mapping study was also done and analyzed for best selected molecules. Additionally, principal component analysis (PCA) was used to examine how the general motion of the protein changed. The results showed quercetin and myricetin to be potential inhibitors of AChE and alpha-amyrin and beta-chlorogenin to be potential inhibitors of BuChE, exhibiting best binding energies comparable to those of donepezil, used as a positive control. The multiple descriptors from the simulation study, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bond, radius of gyration (Rg), and solvent-accessible surface areas (SASA), confirm the stable nature of the protein-ligand complexes. Molecular mechanic Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations indicated the energetically favorable binding of the ligands to the protein. Finally, according to pharmacokinetic properties and drug likeness, characteristics showed that quercetin and myricetin for AChE and alpha-amyrin and beta-chlorogenin for BuChE were found to be the most effective agents for treating the AD.
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Affiliation(s)
- Md. Murshid Alom
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Rejwana Parvin Bonna
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Ariful Islam
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Wasim Alom
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Ekhtiar Rahman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Khalekuzzaman
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Rashed Zaman
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md. Asadul Islam
- Professor O.I Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
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Baren MH, Ibrahim SA, Al-Rooqi MM, Ahmed SA, El-Gamil MM, Hekal HA. A new class of anticancer activity with computational studies for a novel bioactive aminophosphonates based on pyrazole moiety. Sci Rep 2023; 13:14680. [PMID: 37673913 PMCID: PMC10482913 DOI: 10.1038/s41598-023-40265-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023] Open
Abstract
The present study involves synthesis a new series of α-aminophosphonates 2a-f and 4a-d derivatives in good yield with a simple workup via Kabachnik-Fields reaction in the presence of lithium perchlorate as Lewis acid catalyst. All the newly synthesized compounds were confirmed using various physical, spectroscopic, and analytical data. The in vitro anticancer activities of each compound were evaluated against colorectal carcinoma Colon cancer (HCT-116) and Epdermoid carcinoma (HEP2) and also Human lung fibroblast normal cell line (WI38) compared with Doxorubicin. The results showed that Compounds 2a, 4b and 4d exhibited more potent inhibitory activity for Epdermoid Carcinoma (HEP2) compared with doxorubicin. For colon carcinoma cells (HCT-116) Compounds 2a, 2d and 4b gave the strongest activity among all compounds compared with doxorubicin. Moreover, all designed structures were docked into the active site of VEGFR2 and FGFR1 proteins. The result reveals that compound 2b and have the strongest inhibitory activity of the VEGFR2 and FGFR1 proteins indicating that these substances might conceivably operate as VEGFR2 and FGFR1 inhibitors and hence might take role in anticancer activities with various binding interactions. The 3D-QSAR models produced strong statistical results since they were defined by PLS factors 4 and confirmed by parameters as R2, R2 CV, Stability, F-value, P-value, RMSE, Q2, and Pearson-r.
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Affiliation(s)
- Mohamed H Baren
- Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Seham A Ibrahim
- Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Munirah M Al-Rooqi
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, 21955, Saudi Arabia.
| | - Mohammed M El-Gamil
- Department of Toxic and Narcotic Drug, Forensic Medicine, Mansoura Laboratory, Medico legal Organization, Ministry of Justice, Mansoura, Egypt
| | - Hend A Hekal
- Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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9
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Shalaby MA, Fahim AM, Rizk SA. Microwave-assisted synthesis, antioxidant activity, docking simulation, and DFT analysis of different heterocyclic compounds. Sci Rep 2023; 13:4999. [PMID: 36973332 PMCID: PMC10042854 DOI: 10.1038/s41598-023-31995-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
In this investigation, pressure microwave irradiation was used to clarify the activity of 1-(2-hydroxyphenyl)-3-(4-methylphenyl)prop-2-en-1-one (3) towards several active methylene derivatives utilized the pressurized microwave irradiation as green energy resource . Chalcone 3 was allowed to react with ethyl cyanoacetate, acetylacetone, and thioglycolic acid; respectively, at 70 °C with pressure under microwave reaction condition to afford the corresponding 2-hydroxyphenylcyanopyridone, 2-hydroxyphenyl acetylcyclohexanone, and thieno[2,3-c]chromen-4-one derivatives respectively. Moreover, the reaction of chalcone 3 with hydrogen peroxide with stirring affords the corresponding chromen-4-one derivative. All the synthesized compounds were confirmed through spectral tools such as FT-IR, 1HNMR, 13CNMR, and mass spectrum. Furthermore, the synthesized heterocycles were exhibited excellent antioxidant activity and comparable with vitamin C, where the presence of the OH group increases the scavenger radical inhibition. Furthermore, the biological activity of compound 12 was demonstrated through molecular docking stimulation using two proteins, PDBID: 1DH2 and PDBID: 3RP8, which showed that compound 12 possesses greater binding energy and a shorter bond length comparable with ascorbic acid. Also, the compounds were optimized through DFT/B3LYP/6-31G (d,p) basis set and identification of their physical descriptors, whereas the compound 12 was confirmed through X-Ray single structure with Hirsh field analysis of the compound to know the hydrogen electrostatic bond interaction, and correlated with the optimized structure by comparing their bond length, bond angle, FT-IR, and NMR, which gave excellent correlation.
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Affiliation(s)
- Mona A Shalaby
- Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, P.O. 11566, Cairo, Egypt
| | - Asmaa M Fahim
- Green Chemistry Department, National Research Centre Dokki, P.O. Box 12622, Cairo, Egypt.
| | - Sameh A Rizk
- Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, P.O. 11566, Cairo, Egypt
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10
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Razgonova MP, Cherevach EI, Tekutyeva LA, Fedoreyev SA, Mishchenko NP, Tarbeeva DV, Demidova EN, Kirilenko NS, Golokhvast K. Maackia amurensis Rupr. et Maxim.: Supercritical CO 2 Extraction and Mass Spectrometric Characterization of Chemical Constituents. Molecules 2023; 28:molecules28052026. [PMID: 36903272 PMCID: PMC10004358 DOI: 10.3390/molecules28052026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Three types of extraction were used to obtain biologically active substances from the heartwood of M. amurensis: supercritical CO2 extraction, maceration with EtOH, and maceration with MeOH. The supercritical extraction method proved to be the most effective type of extraction, giving the highest yield of biologically active substances. Several experimental conditions were investigated in the pressure range of 50-400 bar, with 2% of ethanol as co-solvent in the liquid phase at a temperature in the range of 31-70 °C. The most effective extraction conditions are: pressure of 100 bar and a temperature of 55 °C for M. amurensis heartwood. The heartwood of M. amurensis contains various polyphenolic compounds and compounds of other chemical groups with valuable biological activity. Tandem mass spectrometry (HPLC-ESI-ion trap) was applied to detect target analytes. High-accuracy mass spectrometric data were recorded on an ion trap equipped with an ESI source in the modes of negative and positive ions. The four-stage ion separation mode was implemented. Sixty-six different biologically active components have been identified in M. amurensis extracts. Twenty-two polyphenols were identified for the first time in the genus Maackia.
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Affiliation(s)
- Mayya P. Razgonova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, B. Morskaya 42-44, 190000 Saint Petersburg, Russia
- Department of Pharmacy and Pharmacology, School of Biomedicine, Far Eastern Federal University, Sukhanova 8, 690950 Vladivostok, Russia
- Correspondence:
| | - Elena I. Cherevach
- Department of Pharmacy and Pharmacology, School of Biomedicine, Far Eastern Federal University, Sukhanova 8, 690950 Vladivostok, Russia
| | - Lyudmila A. Tekutyeva
- Department of Pharmacy and Pharmacology, School of Biomedicine, Far Eastern Federal University, Sukhanova 8, 690950 Vladivostok, Russia
| | - Sergey A. Fedoreyev
- Department of Pharmacy and Pharmacology, School of Biomedicine, Far Eastern Federal University, Sukhanova 8, 690950 Vladivostok, Russia
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Science, Prospect 100 let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Natalia P. Mishchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Science, Prospect 100 let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Darya V. Tarbeeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Science, Prospect 100 let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Ekaterina N. Demidova
- Department of Pharmacy and Pharmacology, School of Biomedicine, Far Eastern Federal University, Sukhanova 8, 690950 Vladivostok, Russia
| | - Nikita S. Kirilenko
- Department of Pharmacy and Pharmacology, School of Biomedicine, Far Eastern Federal University, Sukhanova 8, 690950 Vladivostok, Russia
| | - Kirill Golokhvast
- Department of Pharmacy and Pharmacology, School of Biomedicine, Far Eastern Federal University, Sukhanova 8, 690950 Vladivostok, Russia
- Laboratory of Supercritical Fluid Research and Application in Agrobiotechnology, The National Research Tomsk State University, Lenin Str. 36, 634050 Tomsk, Russia
- Siberian Federal Scientific Centre of Agrobiotechnology, Centralnaya, Presidium, 633501 Krasnoobsk, Russia
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11
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An integrated computational approach towards the screening of active plant metabolites as potential inhibitors of SARS-CoV-2: an overview. Struct Chem 2022; 34:1073-1104. [PMID: 36212707 PMCID: PMC9526463 DOI: 10.1007/s11224-022-02066-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Abstract
COVID-19 and its causative organism SARS-CoV-2 paralyzed the world and was designated a pandemic by the World Health Organization in March 2020. The worldwide health system is trying to discover an effective therapeutic measure since no clinically authorized medications are present. Screening of plant-derived pharmaceuticals may be a viable technique to fight COVID-19 in this vital situation. This review discusses the potential application of in silico approaches in developing new therapeutic molecules related to preventing SARS-CoV-2 infection. Also, it describes the binding affinity of various phytoconstituents with distinct SARS-CoV-2 target sites. In this perspective, an extensive literature survey was carried out to find the potential phytoconstituents to develop new therapeutic entities to treat COVID-19 in different online academic databases and books. Data retrieved from databases were analyzed and interpreted to conclude that many phytochemicals will bind with the 3-chymotrypsin-like (3CLpro) and papain-like proteases (PLpro), spike glycoprotein, ACE-2, NSP15-endoribonuclease, and E protein targets of SARS-CoV-2 main protease using in silico molecular docking approach. The present investigations reveal that phytoconstituents such as curcumin, apigenin, chrysophanol, and gingerol are significantly binding with spike glycoprotein; laurolistine, acetoside, etc. are bound with Mpro for anti-SARS-CoV-2 therapies. Using virtual applications of in silico studies, the current study constitutes a progressive data analysis on the mechanism of binding efficiency of distinct classes of plant metabolites against the active sites of SARS-CoV-2. Furthermore, the current review also demonstrates the fundamental necessity of the alternative and complementary medicine for future therapeutic uses of phytoconstituents by phytochemists in the fight against COVID-19.
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12
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Synthesis, biological evaluation, and bioinformatics analysis of indole analogs on AChE and GST activities. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02974-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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14
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Cetin A, Bursal E, Türkan F. 2-methylindole analogs as cholinesterases and glutathione S-transferase inhibitors: Synthesis, biological evaluation, molecular docking, and pharmacokinetic studies. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103449] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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15
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García-Gutiérrez P, Zubillaga RA, Ibarra IA, Martínez A, Vargas R, Garza J. Non-conventional interactions of N3 inhibitor with the main protease of SARS-CoV and SARS-CoV-2. Comput Struct Biotechnol J 2021; 19:4669-4675. [PMID: 34401047 PMCID: PMC8357482 DOI: 10.1016/j.csbj.2021.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 12/21/2022] Open
Abstract
The extensive spread of COVID-19 in every continent shows that SARS-CoV-2 virus has a higher transmission rate than SARS-CoV virus which emerged in 2002. This results in a global pandemic that is difficult to control. In this investigation, we analyze the interaction of N3 inhibitor and the main protease of SARS-CoV and SARS-CoV-2 by quantum chemistry calculations. Non-covalent interactions involved in these systems were studied using a model of 469 atoms. Density Functional Theory and Quantum Theory of Atoms in Molecules calculations lead us to the conclusion that non-conventional hydrogen bonds are important to describe attractive interactions in these complexes. The energy of these non-conventional hydrogen bonds represents more than a half of the estimated interaction energy for non-covalent contacts. This means that hydrogen bonds are crucial to correctly describe the bonds between inhibitors and the main proteases. These results could be useful for the design of new drugs, since non-covalent interactions are related to possible mechanisms of action of molecules used against these viruses.
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Affiliation(s)
- Ponciano García-Gutiérrez
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa 09340, Ciudad de México, Mexico
| | - Rafael A. Zubillaga
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa 09340, Ciudad de México, Mexico
| | - Ilich A. Ibarra
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior S. N., Ciudad Universitaria, Coyoacán 04510, Ciudad de México, Mexico
| | - Ana Martínez
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior S. N., Ciudad Universitaria, Coyoacán 04510, Ciudad de México, Mexico
| | - Rubicelia Vargas
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa 09340, Ciudad de México, Mexico
| | - Jorge Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa 09340, Ciudad de México, Mexico
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