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Umar AK, Roy D, Abdalla M, Modafer Y, Al-Hoshani N, Yu H, Zothantluanga JH. In-silico screening of Acacia pennata and Bridelia retusa reveals pinocembrin-7-O-β-D-glucopyranoside as a promising β-lactamase inhibitor to combat antibiotic resistance. J Biomol Struct Dyn 2024; 42:8800-8812. [PMID: 37587843 DOI: 10.1080/07391102.2023.2248272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
The β-lactamase of Pseudomonas aeruginosa is known to degrade β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems. With the discovery of an extended-spectrum β-lactamase in a clinical isolate of P. aeruginosa, the bacterium has become multi-drug resistant. In this study, we aim to identify new β-lactamase inhibitors by virtually screening a total of 43 phytocompounds from two Indian medicinal plants. In the molecular docking studies, pinocembrin-7-O-β-D-glucopyranoside (P7G) (-9.6 kcal/mol) from Acacia pennata and ellagic acid (EA) (-9.2 kcal/mol) from Bridelia retusa had lower binding energy than moxalactam (-8.4 kcal/mol). P7G and EA formed 5 (Ser62, Asn125, Asn163, Thr209, and Ser230) and 4 (Lys65, Ser123, Asn125, and Glu159) conventional hydrogens bonds with the active site residues. 100 ns MD simulations revealed that moxalactam and P7G (but not EA) were able to form a stable complex. The binding free energy calculations further revealed that P7G (-59.6526 kcal/mol) formed the most stable complex with β-lactamase when compared to moxalactam (-46.5669 kcal/mol) and EA (-28.4505 kcal/mol). The HOMO-LUMO and other DFT parameters support the stability and chemical reactivity of P7G at the active site of β-lactamase. P7G passed all the toxicity tests and bioavailability tests indicating that it possesses drug-likeness. Among the studied compounds, we identified P7G of A. pennata as the most promising phytocompound to combat antibiotic resistance by potentially inhibiting the β-lactamase of P. aeruginosa.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abd Kakhar Umar
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Dhritiman Roy
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - Yosra Modafer
- Department of Biology, Faculty of Science, Jazan University, Jazan, Saudi Arabia
| | - Nawal Al-Hoshani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Han Yu
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
- Department of Computational Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
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2
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Sabarathinam S, Jayaraman A, Venkatachalapathy R. Computational exploration of Ganoderma lucidum metabolites as potential anti-atherosclerotic agents: Insights from molecular docking and dynamics simulations. Comput Biol Chem 2024; 112:108160. [PMID: 39098136 DOI: 10.1016/j.compbiolchem.2024.108160] [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: 05/19/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
Ganoderma lucidum is a unique form of fungus utilized in Chinese medicine for various therapies as it exhibits a wide range of pharmacological activity. In this study, the purpose is to evaluate the possible drug-like qualities of the metabolites of G. lucidium as well as the impact that these metabolites have on the pathways involved in atherosclerosis. Throughout our research, a total of 17 compounds were chosen based on their drug-like properties. These compounds were then utilized in the subsequent networking and docking simulations. According to the findings, the compound ganodone has a maximum binding energy of -7.243 Kcal/mol. In terms of the binding energy, it has been discovered that the compound cianidanol has the lowest value. Based on the findings of the molecular docking investigations, it was determined that TNF, AKT1, SRC, and STAT3 exhibited a higher affinity for the complex. To determine this, molecular dynamics simulation was performed for about 100 nanoseconds. Following the completion of the GO functional analysis, it was discovered that the target genes were involved in the processes of protein binding, ATP binding, enzyme binding, and protein tyrosine kinase activity. Overall, the study results provide a view of possible metabolites that may have an impact on disease progression.
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Affiliation(s)
- Sarvesh Sabarathinam
- Center for Global Health Research, Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, India.
| | - Akash Jayaraman
- Certifcate Programme-Analytical Techniques in Herbal Drug Industry, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
| | - Ramesh Venkatachalapathy
- Certifcate Programme-Analytical Techniques in Herbal Drug Industry, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603203, India
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3
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Dubey A, Alanazi AM, Bhardwaj R, Ragusa A. Identification of potential NUDT5 inhibitors from marine bacterial natural compounds via molecular dynamics and free energy landscape analysis. Mol Divers 2024:10.1007/s11030-024-10950-5. [PMID: 39225905 DOI: 10.1007/s11030-024-10950-5] [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: 05/18/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
NUDIX hydrolase 5 (NUDT5) is an enzyme involved in the hydrolysis of nucleoside diphosphates linked to other moieties, such as ADP-ribose. This cofactor is vital in redox reactions and is essential for the activity of sirtuins and poly(ADP-ribose) polymerases, which are involved in DNA repair and genomic stability. It has been shown that NUDT5 activity can also influence NAD+ homeostasis, thereby affecting cancer cell metabolism and survival. In this regard, the discovery of NUDT5 inhibitors has emerged as a potential therapeutic approach in cancer treatment. In this study, we conducted a high-throughput virtual screening of marine bacterial compounds against the NUDT5 enzyme and four molecules were selected based on their docking scores. These compounds established strong interactions within the NUDT5 active site, with molecular analysis highlighting the key role of Trp28A and Trp46B residues. Molecular dynamics simulations over 200 ns indicated a stable behavior, in association with root mean square deviation values always below 3 Å, suggesting conformational stability. Free energy landscape analysis further supported their potential as NUDT5 inhibitors, offering avenues for novel therapeutic strategies against NUDT5-associated breast cancer.
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Affiliation(s)
- Amit Dubey
- Department of Pharmacology, Saveetha Dental College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nādu, 600077, India
- Department of Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, 201310, India
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Rima Bhardwaj
- Department of Chemistry, Poona College, Savitribai Phule Pune University, Pune, India.
| | - Andrea Ragusa
- Institute of Nanotechnology, CNR-Nanotec, Via Monteroni, 73100, Lecce, Italy.
- Department of Life Sciences, Health and Health Professions, Link Campus University, Via del Casale Di San Pio V 44, 00165, Rome, Italy.
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Kim H, Kang Y, Kim S, Park D, Heo SY, Yoo JS, Choi I, N MPA, Ahn JW, Yang JS, Bak N, Kim KK, Lee JY, Choi YK. The host protease KLK5 primes and activates spike proteins to promote human betacoronavirus replication and lung inflammation. Sci Signal 2024; 17:eadn3785. [PMID: 39163389 DOI: 10.1126/scisignal.adn3785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/03/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024]
Abstract
Coronaviruses rely on host proteases to activate the viral spike protein, which facilitates fusion with the host cell membrane and the release of viral genomic RNAs into the host cell cytoplasm. The distribution of specific host proteases in the host determines the host, tissue, and cellular tropism of these viruses. Here, we identified the kallikrein (KLK) family member KLK5 as a major host protease secreted by human airway cells and exploited by multiple human betacoronaviruses. KLK5 cleaved both the priming (S1/S2) and activation (S2') sites of spike proteins from various human betacoronaviruses in vitro. In contrast, KLK12 and KLK13 displayed preferences for either the S2' or S1/S2 site, respectively. Whereas KLK12 and KLK13 worked in concert to activate SARS-CoV-2 and MERS-CoV spike proteins, KLK5 by itself efficiently activated spike proteins from several human betacoronaviruses, including SARS-CoV-2. Infection of differentiated human bronchial epithelial cells (HBECs) with human betacoronaviruses induced an increase in KLK5 that promoted virus replication. Furthermore, ursolic acid and other related plant-derived triterpenoids that inhibit KLK5 effectively suppressed the replication of SARS-CoV, MERS-CoV, and SARS-CoV-2 in HBECs and mitigated lung inflammation in mice infected with MERS-CoV or SARS-CoV-2. We propose that KLK5 is a pancoronavirus host factor and a promising therapeutic target for current and future coronavirus-induced diseases.
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Affiliation(s)
- Hyunjoon Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Yeonglim Kang
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Semi Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Dongbin Park
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Seo-Young Heo
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Ji-Seung Yoo
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Isaac Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Monford Paul Abishek N
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Jae-Woo Ahn
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Jeong-Sun Yang
- Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of Health (KNIH), 187 Osongsaengmyeong2-ro, Heungdeok-gu, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Nayeon Bak
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
- Department of Metabiohealth, Sungkyun Convergence Institute, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Metabiohealth, Sungkyun Convergence Institute, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Joo-Yeon Lee
- Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of Health (KNIH), 187 Osongsaengmyeong2-ro, Heungdeok-gu, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Young Ki Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon 34126, Republic of Korea
- Department of Metabiohealth, Sungkyun Convergence Institute, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
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5
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Panday H, Jha SK, Al-Shehri M, Panda SP, Rana R, Alwathinani NF, Azhar EI, Dwivedi VD, Jha AK. Allosteric inhibition of dengue virus RNA-dependent RNA polymerase by Litsea cubeba phytochemicals: a computational study. J Biomol Struct Dyn 2024; 42:5402-5414. [PMID: 38764132 DOI: 10.1080/07391102.2023.2226759] [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: 02/12/2023] [Accepted: 06/11/2023] [Indexed: 05/21/2024]
Abstract
RNA-dependent RNA polymerase (RdRp) is considered a potential drug target for dengue virus (DENV) inhibition and has attracted attention in antiviral drug discovery. Here, we screened 121 natural compounds from Litsea cubeba against DENV RdRp using various approaches of computer-based drug discovery. Notably, we identified four potential compounds (Ushinsunine, Cassameridine, (+)-Epiexcelsin, (-)-Phanostenine) with good binding scores and allosteric interactions with the target protein. Moreover, molecular dynamics simulation studies were done to check the conformational stability of the complexes under given conditions. Additionally, we performed post-simulation analysis to find the stability of potential drugs in the target protein. The findings suggest Litsea cubeba-derived phytomolecules as a therapeutic solution to control DENV infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hrithika Panday
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Mohammed Al-Shehri
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Nada F Alwathinani
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biology, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit - BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Abhimanyu Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
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6
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Purohit P, Barik D, Agasti S, Panda M, Meher BR. Evaluation of the inhibitory potency of anti-dengue phytocompounds against DENV-2 NS2B-NS3 protease: virtual screening, ADMET profiling and molecular dynamics simulation investigations. J Biomol Struct Dyn 2024; 42:2990-3009. [PMID: 37194462 DOI: 10.1080/07391102.2023.2212798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/28/2023] [Indexed: 05/18/2023]
Abstract
Dengue fever has been a worldwide concern, with 50-100 million new infections each year mainly due to five different serotypes of the Dengue virus (DENV). Designing a perfect anti-dengue agent that can inhibit all the serotypes by distinguishing antigenic differences is quite difficult. Previous anti-dengue researches have included chemical compounds screening against DENV enzymes. The ongoing analysis is meant for investigation of the plant-based compounds as antagonistic to DENV-2 focusing on the specific NS2B-NS3Pro target, a trypsin like serine protease that cuts the DENV polyprotein into separate proteins crucial for viral reproduction. Initially, a virtual library of more than 130 phytocompounds was prepared from previously published reports of plants with anti-dengue properties, which were then virtually screened and shortlisted against the WT, H51N and S135A mutant of DENV-2 NS2B-NS3Pro. The three top-most compounds were viewed as Gallocatechin (GAL), Flavokawain-C (FLV), and Isorhamnetin (ISO) showing docking scores of -5.8, -5.7, -5.7 kcal/mol for WT, -7.5, -6.8, -7.6 kcal/mol for the H51N, and -6.9, -6.5, -6.1 kcal/mol for the S135A mutant protease, respectively. 100 ns long MD simulations and MM-GBSA based free energy calculations were performed on the NS2B-NS3Pro complexes to witness the relative binding affinity of the compounds and favourable molecular interactions network. A comprehensive analysis of the study reveals some promising outcomes with ISO as the topmost compound with favourable pharmacokinetic properties for the WT and mutants (H51N and S135A) as well, suggesting as a novel anti-NS2B-NS3Pro agent with better adapting characters in both the mutants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Debashis Barik
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Sidhartha Agasti
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
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7
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Pan S, Mou C, Chen Z. Red recombination enables a wide variety of markerless manipulation of porcine epidemic diarrhea virus genome to generate recombinant virus. Front Cell Infect Microbiol 2024; 13:1338740. [PMID: 38317792 PMCID: PMC10839022 DOI: 10.3389/fcimb.2023.1338740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a member of the genera Alphacoronavirus that has been associated with acute watery diarrhea and vomiting in swine. Unfortunately, no effective vaccines and antiviral drugs for PEDV are currently available. Reverse genetics systems are crucial tools for these researches. Here, a PEDV full-length cDNA clone was constructed. Furtherly, three PEDV reporter virus plasmids containing red fluorescent protein (RFP), Nano luciferase (Nluc), or green fluorescence protein (GFP) were generated using Red recombination with the GS1783 E. coli strain. These reporter-expressing recombinant (r) PEDVs showed similar growth properties to the rPEDV, and the foreign genes were stable to culture up to P9 in Vero cells. Using the Nluc-expressing rPEDV, the replication of PEDV was easily quantified, and a platform for rapid anti-PEDV drug screening was constructed. Among the three drugs, Bergenin, Umifenovir hydrochloride (Arbidol), and Ganoderma lucidum triterpenoids (GLTs), we found that GLTs inhibited PEDV replication mainly after the stage of virus "Entry". Overall, this study will broaden insight into the method for manipulating the PEDV genome and provide a powerful tool for screening anti-PEDV agents.
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Affiliation(s)
- Shuonan Pan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Chunxiao Mou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
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Zaki MEA, AL-Hussain SA, Al-Mutairi AA, Samad A, Masand VH, Ingle RG, Rathod VD, Gaikwad NM, Rashid S, Khatale PN, Burakale PV, Jawarkar RD. Application of in-silico drug discovery techniques to discover a novel hit for target-specific inhibition of SARS-CoV-2 Mpro's revealed allosteric binding with MAO-B receptor: A theoretical study to find a cure for post-covid neurological disorder. PLoS One 2024; 19:e0286848. [PMID: 38227609 PMCID: PMC10790994 DOI: 10.1371/journal.pone.0286848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/24/2023] [Indexed: 01/18/2024] Open
Abstract
Several studies have revealed that SARS-CoV-2 damages brain function and produces significant neurological disability. The SARS-CoV-2 coronavirus, which causes COVID-19, may infect the heart, kidneys, and brain. Recent research suggests that monoamine oxidase B (MAO-B) may be involved in metabolomics variations in delirium-prone individuals and severe SARS-CoV-2 infection. In light of this situation, we have employed a variety of computational to develop suitable QSAR model using PyDescriptor and genetic algorithm-multilinear regression (GA-MLR) models (R2 = 0.800-793, Q2LOO = 0.734-0.727, and so on) on the data set of 106 molecules whose anti-SARS-CoV-2 activity was empirically determined. QSAR models generated follow OECD standards and are predictive. QSAR model descriptors were also observed in x-ray-resolved structures. After developing a QSAR model, we did a QSAR-based virtual screening on an in-house database of 200 compounds and found a potential hit molecule. The new hit's docking score (-8.208 kcal/mol) and PIC50 (7.85 M) demonstrated a significant affinity for SARS-CoV-2's main protease. Based on post-covid neurodegenerative episodes in Alzheimer's and Parkinson's-like disorders and MAO-B's role in neurodegeneration, the initially disclosed hit for the SARS-CoV-2 main protease was repurposed against the MAO-B receptor using receptor-based molecular docking, which yielded a docking score of -12.0 kcal/mol. This shows that the compound that inhibits SARS-CoV-2's primary protease may bind allosterically to the MAO-B receptor. We then did molecular dynamic simulations and MMGBSA tests to confirm molecular docking analyses and quantify binding free energy. The drug-receptor complex was stable during the 150-ns MD simulation. The first computational effort to show in-silico inhibition of SARS-CoV-2 Mpro and allosteric interaction of novel inhibitors with MAO-B in post-covid neurodegenerative symptoms and other disorders. The current study seeks a novel compound that inhibits SAR's COV-2 Mpro and perhaps binds MAO-B allosterically. Thus, this study will enable scientists design a new SARS-CoV-2 Mpro that inhibits the MAO-B receptor to treat post-covid neurological illness.
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Affiliation(s)
- Magdi E. A. Zaki
- Faculty of Science, Department of Chemistry, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Sami A. AL-Hussain
- Faculty of Science, Department of Chemistry, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Aamal A. Al-Mutairi
- Faculty of Science, Department of Chemistry, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Vijay H. Masand
- Department of Chemistry, Vidya Bharti Mahavidyalaya, Amravati, Maharashtra, India
| | - Rahul G. Ingle
- Datta Meghe College of Pharmacy, DMIHER Deemed University, Wardha, India
| | - Vivek Digamber Rathod
- Department of Chemical Technology, Dr Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | | | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Pravin N. Khatale
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, Maharashtra, India
| | - Pramod V. Burakale
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, Maharashtra, India
| | - Rahul D. Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, Maharashtra, India
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Sajid M, Tur Razia I, Kanwal A, Ahsan M, Tahir RA, Sajid M, Khan MS, Mukhtar N, Parveen G, Sehgal SA. Computational Advancement towards the Identification of Natural Inhibitors for Dengue Virus: A Brief Review. Comb Chem High Throughput Screen 2024; 27:2464-2484. [PMID: 37859315 DOI: 10.2174/0113862073244468230921050703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/19/2023] [Accepted: 08/03/2023] [Indexed: 10/21/2023]
Abstract
Viral infectious illnesses represent a severe hazard to human health due to their widespread incidence worldwide. Among these ailments, the dengue virus (DENV) infection stands out. World Health Organization (WHO) estimates that DENV infection affects ~400 million people each year, with potentially fatal symptoms showing up in 1% of the cases. In several instances, academic and pharmaceutical researchers have conducted several pilot and clinical studies on a variety of topics, including viral epidemiology, structure and function analyses, infection source and route, therapeutic targets, vaccinations, and therapeutic drugs. Amongst Takeda, TAK-003, Sanofi, Dengvaxia®, and Butantan/NIH/Merck, Dengvaxia® (CYD-TDV) is the only licensed vaccination yet; however, the potential inhibitors are under development. The biology and evolution of DENVs are briefly discussed in this review, which also compiles the most recent studies on prospective antiviral targets and antiviral candidates. In conclusion, the triumphs and failures have influenced the development of anti-DENV medications, and the findings in this review article will stimulate more investigation.
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Affiliation(s)
- Muhammad Sajid
- Department of Biotechnology, University of Okara, Okara, Punjab, Pakistan
| | - Iashia Tur Razia
- Department of Biotechnology, University of Okara, Okara, Punjab, Pakistan
| | - Ayesha Kanwal
- Department of Biotechnology, University of Okara, Okara, Punjab, Pakistan
| | - Muhammad Ahsan
- Institute of Environmental and Agricultural Sciences, University of Okara, Okara, Punjab, Pakistan
| | - Rana Adnan Tahir
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Punjab, Pakistan
| | - Muhammad Sajid
- Department of Biotechnology, University of Okara, Okara, Punjab, Pakistan
| | | | - Naila Mukhtar
- Department of Botany, University of Okara, Okara, Punjab, Pakistan
| | - Gulnaz Parveen
- Department of Botany, Women University Swabi, Swabi, KPK, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology, and Bioinformatics, The Islamia University of Bahawalpur, Punjab, Pakistan
- Department of Bioinformatics, University of Okara, Okara, Punjab, Pakistan
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10
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Prabha S, Chauhan P, Warkare S, Pandey KM. A computational investigation of potential plant-based bioactive compounds against drug-resistant Staphylococcus aureus of multiple target proteins. J Biomol Struct Dyn 2023:1-19. [PMID: 38133950 DOI: 10.1080/07391102.2023.2297009] [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: 06/09/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Drug-resistant Staphylococcus aureus (DRSA) poses a significant global health threat, like bacteremia, endocarditis, skin, soft tissue, bone, and joint infections. Nowadays, the resistance against conventional drugs has been a prompt and focused medical concern. The present study aimed to explore the inhibitory potential of plant-based bioactive compounds (PBBCs) against effective target proteins using a computational approach. We retrieved and verified 22 target proteins associated with DRSA and conducted a screening process that involved testing 87 PBBCs. Molecular docking was performed between screened PBBCs and reference drugs with selected target proteins via AutoDock. Subsequently, we filtered the target proteins and top PBBCs based on their binding affinity scores. Furthermore, molecular dynamic simulation was carried out through GROMACS for a duration of 100 ns, and the binding free energy was calculated using the gmx_MMPBSA. The result showed consistent hydrogen bonding interactions among the amino acid residues Ser 149, Arg 151, Thr 165, Thr 216, Glu 239, Ser 240, Ile 14, as well as Asn 18, Gln 19, Lys 45, Thr 46, Tyr 109, with their respective target proteins of the penicillin-binding protein and dihydrofolate reductase complex. Additionally, we assessed the pharmacokinetic properties of screened PBBCs via SwissADME and AdmetSAR. The findings suggest that β-amyrin, oleanolic acid, kaempferol, quercetin, and friedelin have the potential to inhibit the selected target proteins. In future research, both in vitro and in vivo, experiments will be needed to establish these PBBCs as potent antimicrobial drugs for DRSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarit Prabha
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | | | - Sudeesh Warkare
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Khushhali M Pandey
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
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11
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Alabbas AB. Identification of promising methionine aminopeptidase enzyme inhibitors: A combine study of comprehensive virtual screening and dynamics simulation study. Saudi Pharm J 2023; 31:101745. [PMID: 37638221 PMCID: PMC10448168 DOI: 10.1016/j.jsps.2023.101745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/05/2023] [Indexed: 08/29/2023] Open
Abstract
Methionine aminopeptidase (MetAP) enzymes play a critical role in bacterial cell survival by cleaving formyl-methionine initiators at N-terminal of nascent protein, a process which is vital in proper protein folding. This makes MetAP an attractive and novel antibacterial target to unveil promising antibiotics. In this study, the crystal structure of R. prowazekii MetAP was used in structure-based virtual screening of drug libraries such as Asinex antibacterial library and Comprehensive Marine Natural Products Database (CMNPD) to identify promising lead molecules against the enzyme. This shortlisted three drug molecules; BDE-25098678, BDE-30686468 and BDD_25351157 as most potent leads that showed strong binding to the MetAP enzyme. The static docked conformation of the compounds to the MetAP was reevaluated in molecular dynamics simulation studies. The analysis observed the docked complexes as stable structure with no major local or global deviations noticed. These findings suggest the formation of strong intermolecular docked complexes, which showed stable dynamics and atomic level interactions network. The binding free energy analysis predicted net MMGBSA energy of complexes as: BDE-25098678 (-73.41 kcal/mol), BDE-30686468 (-59.93 kcal/mol), and BDD_25351157 (-75.39 kcal/mol). In case of MMPBSA, the complexes net binding energy was as; BDE-25098678 (-77.47 kcal/mol), BDE-30686468 (-69.47 kcal/mol), and BDD_25351157 (-75.6 kcal/mol). Further, the compounds were predicted to follow the famous Lipinski rule of five and have non-toxic, non-carcinogenic and non-mutagenic profile. The screened compounds might be used in experimental test to highlight the real anti- R. prowazekii MetAP activity.
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Affiliation(s)
- Alhumaidi B. Alabbas
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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12
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Mukhtar M, Khan HA, Zaidi NUSS. Exploring the inhibitory potential of Nigella sativa against dengue virus NS2B/NS3 protease and NS5 polymerase using computational approaches. RSC Adv 2023; 13:18306-18322. [PMID: 37333789 PMCID: PMC10273825 DOI: 10.1039/d3ra02613b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/29/2023] [Indexed: 06/20/2023] Open
Abstract
Dengue fever, a highly infectious and rapidly spreading vector borne illness, is classified as a Neglected Tropical Disease (NTD) by WHO because they generally afflict the world's poor and historically have not received as much attention as other diseases. DENV NS2B/NS3 protease and NS5 polymerase are regarded as significant prospective therapeutic targets because of their critical involvement in the viral replication cycle. To date, no specific antiviral agents exist for dengue. The commonly used herbal plant Nigella sativa is known for its antibacterial, antiviral, anti-inflammatory, wound-healing, and dermatological properties. Nevertheless, not enough studies on the antiviral effects of Nigella sativa against DENV are reported. The current study used several prediction techniques to anticipate the oral bioavailability of substances, druglikeness, and non-toxic and non-mutagenic effects which could lead to the development of novel, safer medications. Therefore, the current study was conducted to explore the inhibitory potential of 18 phytochemicals from Nigella sativa against two important enzymes of dengue virus i.e., NS2B/NS3 and NS5. Promising results have been observed for NS2B/NS3 with Taraxerol (-9.1 kcal mol-1), isoquercetin (8.4 kcal mol-1), apigenin, and stigmasterol (-8.3 kcal mol-1). Similarly, NS5 has shown favorable outcomes with apigenin (-9.9 kcal mol-1), rutin (-9.3 kcal mol-1), nigellicine (-9.1 kcal mol-1), and stigmasterol (-8.8 kcal mol-1). MD simulations validated the structural flexibility of the NS2B/NS3-taraxerol and NS5-apigenin docking complexes based on an RMSF value below 5 Å. The study concluded that among the understudied phytocomponents of N. sativa, apigenin, nigellicine, nigellidine, dithymoquinone, taraxerol, campesterol, cycloeucalenol, stigmasterol and beta-sitosterol have been revealed as potential drug candidates, expected to show antiviral activity and promising drug likeliness. Phytochemicals on the short list may serve as inspiration for the creation of new drugs in the future. Further in vitro examination will assist in elucidating the molecular complexity of therapeutic and antiviral capabilities, opening several opportunities for researchers to identify novel medications throughout the drug development process.
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Affiliation(s)
- Mamuna Mukhtar
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) H-12 44000 Islamabad Pakistan
| | - Haris Ahmed Khan
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) H-12 44000 Islamabad Pakistan
- Department of Biotechnology, University of Mianwali 42200 Punjab Pakistan
| | - Najam Us Sahar Sadaf Zaidi
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) H-12 44000 Islamabad Pakistan
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13
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Wang P, Yang G, Shi N, Zhao C, Hu F, Coutts RHA, Kotta-Loizou I, Huang B. A novel partitivirus orchestrates conidiation, stress response, pathogenicity, and secondary metabolism of the entomopathogenic fungus Metarhizium majus. PLoS Pathog 2023; 19:e1011397. [PMID: 37216409 DOI: 10.1371/journal.ppat.1011397] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/01/2023] [Indexed: 05/24/2023] Open
Abstract
Mycoviruses are widely present in all major groups of fungi but those in entomopathogenic Metarhizium spp. remain understudied. In this investigation, a novel double-stranded (ds) RNA virus is isolated from Metarhizium majus and named Metarhizium majus partitivirus 1 (MmPV1). The complete genome sequence of MmPV1 comprises two monocistronic dsRNA segments (dsRNA 1 and dsRNA 2), which encode an RNA-dependent RNA polymerase (RdRp) and a capsid protein (CP), respectively. MmPV1 is classified as a new member of the genus Gammapartitivirus in the family Partitiviridae based on phylogenetic analysis. As compared to an MmPV1-free strain, two isogenic MmPV1-infected single-spore isolates were compromised in terms of conidiation, and tolerance to heat shock and UV-B irradiation, while these phenotypes were accompanied by transcriptional suppression of multiple genes involved in conidiation, heat shock response and DNA damage repair. MmPV1 attenuated fungal virulence since infection resulted in reduced conidiation, hydrophobicity, adhesion, and cuticular penetration. Additionally, secondary metabolites were significantly altered by MmPV1 infection, including reduced production of triterpenoids, and metarhizins A and B, and increased production of nitrogen and phosphorus compounds. However, expression of individual MmPV1 proteins in M. majus had no impact on the host phenotype, suggesting insubstantive links between defective phenotypes and a single viral protein. These findings indicate that MmPV1 infection decreases M. majus fitness to its environment and its insect-pathogenic lifestyle and environment through the orchestration of the host conidiation, stress tolerance, pathogenicity, and secondary metabolism.
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Affiliation(s)
- Ping Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Guogen Yang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Najie Shi
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Cheng Zhao
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Fenglin Hu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Robert H A Coutts
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
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14
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Jiang L, Zhang W, Zhai DD, Wan G, Xia S, Meng J, Shi P, Chen N. Transcriptome profiling and bioinformatic analysis of the effect of ganoderic acid T prevents Sendai virus infection. Gene 2023; 862:147252. [PMID: 36740203 DOI: 10.1016/j.gene.2023.147252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/27/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Ganoderic acid T (GA-T) is an important triterpene of Ganoderma lucidum, which is utilized to treat viral infections. Sendai virus (SeV) is widely studied to determine the molecular biological characteristics of RNA viruses and employed to elucidate the mechanisms governing the innate immune response. However, the comprehensive mechanism governing the antiviral effects of GA-T against SeV infection remains unknown. In this study, SeV-infected host cells were treated with 16.3 μM GA-T, subsequently RNA-seq analysis was performed to screen the differentially expressed genes (DEGs). The RNA-seq data showed that GA-T treatment upregulated 934 DEGs and downregulated 1283 DEGs against viral infection, in particularly, IFNGR1, IL1A, and IL1R1 were upregulated, and mTOR, SMAD3, IFNL2 and IFNL3 were decreased. GO and KEGG analysis illustrated that DEGs were clustered in mTOR and IL-17 signalling pathways. Protein-protein interaction network analysis indicated the high degree of nodes, such as CXCL8, CSF2, CXCL1 and MYD88. Our results indicated that GA-T exerted its antiviral pharmacological effects through inhibition of the mTOR signalling pathway and adjustment of innate immunity system and the inflammatory response involving the IL-17 signalling pathway. Our results may help to elucidate the potential functions and underlying mechanisms governing the antiviral effects of GA-T.
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Affiliation(s)
- Liying Jiang
- Zhoupu Hospital in Pudong New Area & Jiading District Central Hospital Affiliated, Shanghai University of Medicine & Health Sciences Shanghai 201318, PR China
| | - Wei Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Dan-Dan Zhai
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, PR China
| | - Guoqing Wan
- Zhoupu Hospital in Pudong New Area & Jiading District Central Hospital Affiliated, Shanghai University of Medicine & Health Sciences Shanghai 201318, PR China
| | - Shengli Xia
- Zhoupu Hospital in Pudong New Area & Jiading District Central Hospital Affiliated, Shanghai University of Medicine & Health Sciences Shanghai 201318, PR China
| | - Jihong Meng
- Department of Microbiology and Immunology, School of Medicine, Southeast University, 87 Dingjiaqiao Road, Nanjing 210009, PR China
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
| | - Nianhong Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China; Center Lab of Longhua Branch and Department of Infectious Disease, Shenzhen People's Hospital, 2nd Clinical Medical College of Jinan University, and Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Medicine School of Shenzhen University, Shenzhen 518020, PR China.
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15
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Rašeta M, Mišković J, Čapelja E, Zapora E, Petrović Fabijan A, Knežević P, Karaman M. Do Ganoderma Species Represent Novel Sources of Phenolic Based Antimicrobial Agents? Molecules 2023; 28:3264. [PMID: 37050027 PMCID: PMC10096548 DOI: 10.3390/molecules28073264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Ganoderma species have been recognized as potential antimicrobial (AM) agents and have been used in traditional Chinese medicine (TCM) for a long time. The aim of this study is to examine the AM potential of autochthonous Ganoderma species (G. applanatum, G. lucidum, G. pfeifferi and G. resinaceum) from Serbia. The extraction of fungal material was prepared in different solvents (ethanol-EtOH, water-H2O, chloroform-CHCl3). Antibacterial activity (ABA) was determined using disk-diffusion, agar-well diffusion, and micro-dilution method, while for antifungal properties disk-diffusion and pour plate method were applied. Antiviral activity was tested on model DNA virus LK3 and determined by plaque assay. Statistical PCA analysis was applied for detection of correlation effects of phenolics and AM activities, while LC-MS/MS was performed for phenolics quantification. G. resinaceum CHCl3 extract expressed the most potent ABA against P. aeruginosa (MIC = 6.25 mg/mL), probably due to presence of flavonoids and 2,5-dihydroxybenzoic acid. Among H2O extracts, the highest ABA was determined for G. pfeifferi against both E. coli and S. aureus (21 and 19 mm, respectively). EtOH extracts of G. pfeifferi and G. resinaceum were the most effective against A. niger (23.8 and 20.15 mm, respectively), with special impact of phenolic acids and flavonoid isorhamnetin, while C. albicans showed the lowest susceptibility. The most potent antiviral inhibitor was G. lucidum (70.73% growth inhibition) due to the high amount of phenolic acids. To the best of our knowledge, this is the first report of a methodical AM profile of G. pfeifferi and G. resinaceum from the Balkan region including PCA analysis.
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Affiliation(s)
- Milena Rašeta
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Jovana Mišković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Eleonora Čapelja
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Ewa Zapora
- Institute of Forest Sciences, Białystok University of Technology, Wiejska 45E, 15-351 Białystok, Poland
| | - Aleksandra Petrović Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Petar Knežević
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Maja Karaman
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
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16
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Blundell R, Camilleri E, Baral B, Karpiński TM, Neza E, Atrooz OM. The Phytochemistry of Ganoderma Species and their Medicinal Potentials. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2023; 51:859-882. [PMID: 36999543 DOI: 10.1142/s0192415x23500404] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
The Ganoderma genus is known for its diverse use as a functional food and therapeutic agent. This fungus has over 428 species, with Ganoderma lucidum being the most studied. The Ganoderma species produce several secondary metabolites and bioactive compounds like polysaccharides, phenols, and triterpenes, which are largely responsible for their therapeutic properties. Throughout this review, several extracts obtained from Ganoderma species have been studied to delve into their therapeutic characteristics and mechanisms. Such properties like immunomodulation, antiaging, antimicrobial, and anticancer activities have been demonstrated by several Ganoderma species and are supported by a large body of evidence. Although its phytochemicals play a vital role in its therapeutic properties, identifying the therapeutic potentials of fungal-secreted metabolites for human health-promoting benefits is a challenging task. Identification of novel compounds with distinct chemical scaffolds and their mechanism of action could help suppress the spread of rising pathogens. Thus, this review provides an updated and comprehensive overview of the bioactive components in different Ganoderma species and the underlying physiological mechanisms.
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Affiliation(s)
- Renald Blundell
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD2080 Imsida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, MSD2080 Imsida, Malta
| | - Emma Camilleri
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD2080 Imsida, Malta
| | - Bikash Baral
- Institute of Biological Resources (IBR), Kathmandu, Nepal
| | - Tomasz M Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Rokietnicka 10, 60-806 Poznań, Poland
| | - Edlira Neza
- Western Balkans University, Autostrada Tirane-Durres km 7, Albania
| | - Omar M Atrooz
- Department of Biological Sciences, Mutah University, P. O. Box (7), Mutah, Jordan
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17
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de Sousa ALM, Rizaldo Pinheiro R, Furtado Araujo J, Mesquita Peixoto R, de Azevedo DAA, Cesar Lima AM, Marques Canuto K, Vasconcelos Ribeiro PR, de Queiroz Souza AS, Rocha Souza SC, de Amorim SL, Paula Amaral G, de Souza V, de Morais SM, Andrioli A, da Silva Teixeira MF. In vitro antiviral effect of ethanolic extracts from Azadirachta indica and Melia azedarach against goat lentivirus in colostrum and milk. Sci Rep 2023; 13:4677. [PMID: 36949145 PMCID: PMC10031174 DOI: 10.1038/s41598-023-31455-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
This study aimed to evaluate, in vitro, the use of leaf extracts of Azadirachta indica (A. indica) and Melia azedarach (M. azedarach) as antivirals against caprine lentivirus (CLV) in colostrum and milk of goat nannies. These were collected from eight individuals and infected with the standard strain of CLV. Samples were then subdivided into aliquots and treated with 150 µg/mL of crude extract, and with ethyl acetate and methanol fractions for 30, 60, and 90 min. Next, somatic cells from colostrum and milk were co-cultured with cells from the ovine third eyelid. After this step, viral titers of the supernatants collected from treatments with greater efficacy in co-culture were assessed. The organic ethyl acetate fractions of both plants at 90 min possibly inhibited the viral activity of CLV by up to a thousandfold in colostrum. In milk, this inhibition was up to 800 times for the respective Meliaceae. In conclusion, the ethanolic fraction of ethyl acetate from both plants demonstrated efficacy against CLV in samples from colostrum and milk when subjected to treatment, which was more effective in colostrum.
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Affiliation(s)
- Ana Lidia Madeira de Sousa
- Laboratory of Virology (LABOVIR), State University of Ceará (UECE), Fortaleza, CE, Brazil.
- Faculdade Educar da Ibiapaba, Ípu, CE, Brazil.
| | | | | | - Renato Mesquita Peixoto
- Vale do Salgado University Center (UNIVS), Icó, CE, Brazil
- Terra Nordeste College (FATENE), Caucaia, CE, Brazil
| | | | - Ana Milena Cesar Lima
- Scholarship for Regional Scientific Development of the National Council for Scientific and Technological Development (DCR-CNPq/FUNCAP), Level C, Embrapa Goats and Sheep, Sobral, CE, Brazil
| | - Kirley Marques Canuto
- Multiuser Laboratory of Natural Products Chemistry, Embrapa Tropical Agroindustry, Fortaleza, CE, Brazil
| | | | | | | | - Sara Lucena de Amorim
- Department of Veterinary Medicine, Federal University of Rondônia, Rolim de Moura, RO, Brazil
| | | | - Viviane de Souza
- Laboratory of Microbiology, Embrapa Goats and Sheep, Sobral, CE, Brazil
| | - Selene Maia de Morais
- Laboratory of Chemistry and Natural Products (LQPN), Ceará State University, Fortaleza, CE, Brazil
| | - Alice Andrioli
- Laboratory of Virology, Embrapa Goats and Sheep, Sobral, CE, Brazil
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18
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Wong KKV, Roney M, Uddin N, Imran S, Gazali AM, Zamri N, Rullah K, Aluwi MFFM. Usnic acid as potential inhibitors of BCL2 and P13K protein through network pharmacology-based analysis, molecular docking and molecular dynamic simulation. J Biomol Struct Dyn 2023; 41:13632-13645. [PMID: 36794726 DOI: 10.1080/07391102.2023.2178506] [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: 07/25/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
Usnic acid (UA) lately piqued the interest of researchers for its extraordinary biological characteristics, including anticancer activity. Here, the mechanism was clarified through network pharmacology,molecular docking and molecular dynamic simulation. Sixteen proteins were selected through network pharmacology study as they are probable to interact with UA. Out of these proteins, 13 were filtered from PPI network analysis based on their significance of interactions (p < 0.05). KEGG pathway analysis has also aided us in determining the three most significant protein targets for UA, which are BCL2, PI3KCA and PI3KCG. Therefore molecular docking and molecular dynamic (MD) simulations throughout 100 ns were performed for usnic acid onto the three proteins mentioned. However, UA's docking score in all proteins is lower than their co-crystalised ligand, especially for BCL2 (-36.5158 kcal/mol) and PI3KCA (-44.5995 kcal/mol) proteins. The only exception is PI3KCG which has comparable results with the co-crystallised ligand with (-41.9351 kcal/mol). Furthermore, MD simulation has also revealed that usnic acid does not stay fit in the protein throughout the simulation trajectory for PI3KCA protein evident from RMSF and RMSD plots. Nevertheless, it still poses good ability in inhibiting BCL2 and PI3KCG protein in MD simulation. In the end, usnic acid has exhibited good potential in the inhibition of PI3KCG proteins, rather than the other proteins mentioned. Thus further study on structural modification of usnic acid could enhance the ability of usnic acid in the inhibition of PI3KCG as anti-colorectal and anti-small cell lung cancer drug candidate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K K V Wong
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Pahang, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Pahang, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery, UiTM Selangor, Kampus Puncak Alam, Bandar Puncak Alam, Malaysia
| | - Ahmad Mahfuz Gazali
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Pahang, Malaysia
| | - Normaiza Zamri
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Pahang, Malaysia
| | - Kamal Rullah
- Drug Discovery and Synthetic Chemistry Research Group, Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Pahang, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang, Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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19
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Norshidah H, Leow CH, Ezleen KE, Wahab HA, Vignesh R, Rasul A, Lai NS. Assessing the potential of NS2B/NS3 protease inhibitors biomarker in curbing dengue virus infections: In silico vs. In vitro approach. Front Cell Infect Microbiol 2023; 13:1061937. [PMID: 36864886 PMCID: PMC9971573 DOI: 10.3389/fcimb.2023.1061937] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023] Open
Abstract
An increase in the occurrence of viral infectious diseases is a global concern for human health. According to a WHO report, dengue virus (DENV) is one of the most common viral diseases affecting approximately 400 million people annually, with worsening symptoms in nearly 1% of cases. Both academic and industrial researchers have conducted numerous studies on viral epidemiology, virus structure and function, source and route of infection, treatment targets, vaccines, and drugs. The development of CYD-TDV or Dengvaxia® vaccine has been a major milestone in dengue treatment. However, evidence has shown that vaccines have some drawbacks and limitations. Therefore, researchers are developing dengue antivirals to curb infections. DENV NS2B/NS3 protease is a DENV enzyme essential for replication and virus assembly, making it an interesting antiviral target. For faster hit and lead recognition of DENV targets, methods to screen large number of molecules at lower costs are essential. Similarly, an integrated and multidisciplinary approach involving in silico screening and confirmation of biological activity is required. In this review, we discuss recent strategies for searching for novel DENV NS2B/NS3 protease inhibitors from the in silico and in vitro perspectives, either by applying one of the approaches or by integrating both. Therefore, we hope that our review will encourage researchers to integrate the best strategies and encourage further developments in this area.
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Affiliation(s)
- Harun Norshidah
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia,Universiti Kuala Lumpur-Royal College of Medicine Perak, Ipoh, Perak, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Ramachandran Vignesh
- Universiti Kuala Lumpur-Royal College of Medicine Perak, Ipoh, Perak, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
| | - Azhar Rasul
- Department of Zoology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Ngit Shin Lai
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
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20
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Teramoto T, Choi KH, Padmanabhan R. Flavivirus proteases: The viral Achilles heel to prevent future pandemics. Antiviral Res 2023; 210:105516. [PMID: 36586467 PMCID: PMC10062209 DOI: 10.1016/j.antiviral.2022.105516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022]
Abstract
Flaviviruses are important human pathogens and include dengue (DENV), West Nile (WNV), Yellow fever virus (YFV), Japanese encephalitis (JEV) and Zika virus (ZIKV). DENV, transmitted by mosquitoes, causes diseases ranging in severity from mild dengue fever with non-specific flu-like symptoms to fatal dengue hemorrhagic fever and dengue shock syndrome. DENV infections are caused by four serotypes, DENV1-4, which interact differently with antibodies in blood serum. The incidence of DENV infection has increased dramatically in recent decades and the CDC estimates 400 million dengue infections occur each year, resulting in ∼25,000 deaths mostly among children and elderly people. Similarly, ZIKV infections are caused by infected mosquito bites to humans, can be transmitted sexually and through blood transfusions. If a pregnant woman is infected, the virus can cross the placental barrier and can spread to her fetus, causing severe brain malformations in the child including microcephaly and other birth defects. It is noteworthy that the neurological manifestations of ZIKV were also observed in DENV endemic regions, suggesting that pre-existing antibody response to DENV could augment ZIKV infection. WNV, previously unknown in the US (and known to cause only mild disease in Middle East), first arrived in New York city in 1999 (NY99) and spread throughout the US and Canada by Culex mosquitoes and birds. WNV is now endemic in North America. Thus, emerging and re-emerging flaviviruses are significant threat to human health. However, vaccines are available for only a limited number of flaviviruses, and antiviral therapies are not available for any flavivirus. Hence, there is an urgent need to develop therapeutics that interfere with essential enzymatic steps, such as protease in the flavivirus lifecycle as these viruses possess significant threat to future pandemics. In this review, we focus on our E. coli expression of NS2B hydrophilic domain (NS2BH) covalently linked to NS3 protease domain (NS3Pro) in their natural context which is processed by the combined action of both subunits of the NS2B-NS3Pro precursor. Biochemical activities of the viral protease such as solubility and autoproteolysis of NS2BH-NS3Pro linkage depended on the C-terminal portion of NS2BH linked to the NS3Pro domain. Since 2008, we also focus on the use of the recombinant protease in high throughput screens and characterization of small molecular compounds identified in these screens.
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Affiliation(s)
- Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
| | - Kyung H Choi
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47406, USA.
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
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21
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Zothantluanga JH, Umar AK, Lalhlenmawia H, Vinayagam S, Borthakur MS, Patowary L, Tayeng D. Computational screening of phytochemicals for anti-parasitic drug discovery. PHYTOCHEMISTRY, COMPUTATIONAL TOOLS AND DATABASES IN DRUG DISCOVERY 2023:257-283. [DOI: 10.1016/b978-0-323-90593-0.00005-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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22
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Exploration of Potent Antiviral Phytomedicines from Lauraceae Family Plants against SARS-CoV-2 Main Protease. Viruses 2022; 14:v14122783. [PMID: 36560787 PMCID: PMC9785681 DOI: 10.3390/v14122783] [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: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
A new Coronaviridae strain, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), emerged from Wuhan city of China and caused one of the substantial global health calamities in December 2019. Even though several vaccines and drugs have been developed worldwide since COVID-19, a cost-effective drug with the least side effects is still unavailable. Currently, plant-derived compounds are mostly preferred to develop antiviral therapeutics due to its less toxicity, easy access, and cost-effective characteristics. Therefore, in this study, 124 phytochemical compounds from plants of Lauraceae family with medicinal properties were virtually screened against SARS-CoV-2 Mpro. Identification of four phytomolecules, i.e., cassameridine, laetanine, litseferine and cassythicine, with docking scores -9.3, -8.8, -8.6, and -8.6 kcal/mol, respectively, were undertaken by virtual screening, and molecular docking. Furthermore, the molecular dynamic simulation and essential dynamics analysis have contributed in understanding the stability and inhibitory effect of these selected compounds. These phytomolecules can be considered for further in vitro and in vivo experimental study to develop anti-SARS-CoV-2 therapeutics targeting the main protease (Mpro).
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23
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Chang SN, Keretsu S, Kang SC. Evaluation of decursin and its isomer decursinol angelate as potential inhibitors of human glutamate dehydrogenase activity through in silico and enzymatic assay screening. Comput Biol Med 2022; 151:106287. [PMID: 36455296 DOI: 10.1016/j.compbiomed.2022.106287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/09/2022] [Accepted: 11/06/2022] [Indexed: 11/16/2022]
Abstract
Glutaminolysis is a typical hallmark of malignant tumors across different cancers. Glutamate dehydrogenase (GDH, GLUD1) is one such enzyme involved in the conversion of glutamate to α-ketoglutarate. High levels of GDH are associated with numerous diseases and is also a prognostic marker for predicting metastasis in colorectal cancer. Therefore, inhibiting GDH can be a crucial therapeutic target. Here in this study, we performed molecular docking analysis of 8 different plants derived single compounds collected from pubChem database for screening and selected decursin (DN) and decursinol angelate (DA). We performed molecular dynamics simulation (MD), monitored the stability, interaction for protein and docked ligand at 50 ns, and evaluated the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation on the twoselected compounds along with a standard inhibitor epigallocatechin gallate (EGCG) as reference. The final results showed the formation of stable hydrogen bond interactions by DN and DA in the residues of R400 and Y386 at the ADP activation site of GDH, which was important for the selective inhibition of GDH activity. Additionally, the total binding energy of DN and DA were -115.5 kJ/mol and -106.2 kJ/mol, which was higher than the standard reference GDH inhibitor EGCG (-92.8 kJ/mol). Furthermore, biochemical analysis for GDH inhibition substantiated our computational results and established DN and DA as novel GDH inhibitor. The percentage of IC50 inhibition for DN and DA were 1.035 μM and 1.432 μM. Conclusively, DN and DA can be a novel therapeutic drug for inhibition of glutamate dehydrogenase.
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Affiliation(s)
| | - Seketoulie Keretsu
- Department of Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Sun Chul Kang
- Department of Biotechnology, Daegu University, Gyeongsan, 38453, South Korea.
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24
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Lucidumol A, Purified Directly from Ganoderma lucidum, Exhibits Anticancer Effect and Cellular Inflammatory Response in Colorectal Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:7404493. [DOI: 10.1155/2022/7404493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022]
Abstract
Colorectal cancer (CRC) is a deadly disease regardless of sex, and a few therapeutic approaches have been fully developed at advanced stages, even if some strategies have durable clinical benefits, such as immunotherapy and chemotherapy. Ganoderma lucidum has been recognized as an organism that suppresses tumors and inflammation; however, the molecular mechanisms induced by a triterpenoid in Ganoderma lucidum, Lucidumol A, have not yet been fully explored in CRC and inflammatory responses. To this end, we extracted Lucidumol A from Ganoderma lucidum and analyzed its anticancer effect and anti-inflammatory potential in CRC cell lines and RAW264.7 macrophage-derived cell lines, respectively. A series of in vitro experiments including cell survival, wound healing, and migration assays were performed to determine the role of Lucidumol A in the CRC cell line. We also analyzed inflammatory responses using qRT-PCR, Western Blot, and ELISA in RAW 264.7 macrophaged-derived cell lines exposed to various concentrations of Lucidumol A. Lucidumol A efficiently suppressed the metastatic potential of CRC at very low concentrations. Furthermore, significant anti-inflammatory activities were observed in Lucidumol A-treated RAW264.7 cells through modulation of inflammation-associated marker genes and cytokines. In conclusion, Lucidumol A plays an important role in Ganoderma lucidum-dependent tumor suppression and anti-inflammation, suggesting different strategies to treat CRC patients, and other diseases evoked by proinflammatory cytokines, despite the need to explore further its mechanism of action.
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25
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Montecillo JAV, Bae H. In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity. Sci Rep 2022; 12:18883. [PMID: 36344604 PMCID: PMC9640594 DOI: 10.1038/s41598-022-20461-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel-the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.
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Affiliation(s)
- Jake Adolf V Montecillo
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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26
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Dos Santos Nascimento IJ, da Silva Rodrigues ÉE, da Silva MF, de Araújo-Júnior JX, de Moura RO. Advances in Computational Methods to Discover New NS2B-NS3 Inhibitors Useful Against Dengue and Zika Viruses. Curr Top Med Chem 2022; 22:2435-2462. [PMID: 36415099 DOI: 10.2174/1568026623666221122121330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022]
Abstract
The Flaviviridae virus family consists of the genera Hepacivirus, Pestivirus, and Flavivirus, with approximately 70 viral types that use arthropods as vectors. Among these diseases, dengue (DENV) and zika virus (ZIKV) serotypes stand out, responsible for thousands of deaths worldwide. Due to the significant increase in cases, the World Health Organization (WHO) declared DENV a potential threat for 2019 due to being transmitted by infected travelers. Furthermore, ZIKV also has a high rate of transmissibility, highlighted in the outbreak in 2015, generating consequences such as Guillain-Barré syndrome and microcephaly. According to clinical outcomes, those infected with DENV can be asymptomatic, and in other cases, it can be lethal. On the other hand, ZIKV has severe neurological symptoms in newborn babies and adults. More serious symptoms include microcephaly, brain calcifications, intrauterine growth restriction, and fetal death. Despite these worrying data, no drug or vaccine is approved to treat these diseases. In the drug discovery process, one of the targets explored against these diseases is the NS2B-NS3 complex, which presents the catalytic triad His51, Asp75, and Ser135, with the function of cleaving polyproteins, with specificity for basic amino acid residues, Lys- Arg, Arg-Arg, Arg-Lys or Gln-Arg. Since NS3 is highly conserved in all DENV serotypes and plays a vital role in viral replication, this complex is an excellent drug target. In recent years, computer-aided drug discovery (CADD) is increasingly essential in drug discovery campaigns, making the process faster and more cost-effective, mainly explained by discovering new drugs against DENV and ZIKV. Finally, the main advances in computational methods applied to discover new compounds against these diseases will be presented here. In fact, molecular dynamics simulations and virtual screening is the most explored approach, providing several hit and lead compounds that can be used in further optimizations. In addition, fragment-based drug design and quantum chemistry/molecular mechanics (QM/MM) provides new insights for developing anti-DENV/ZIKV drugs. We hope that this review offers further helpful information for researchers worldwide and stimulates the use of computational methods to find a promising drug for treating DENV and ZIKV.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Department of Pharmacy, Estácio of Alagoas College, Maceió, Brazil.,Department of Pharmacy, Cesmac University Center, Maceió, Brazil.,Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
| | | | - Manuele Figueiredo da Silva
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - Ricardo Olimpio de Moura
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
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27
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Xu J, Yang W, Pan Y, Xu H, He L, Zheng B, Xie Y, Wu X. Lucidenic acid A inhibits the binding of hACE2 receptor with spike protein to prevent SARS-CoV-2 invasion. Food Chem Toxicol 2022; 169:113438. [PMID: 36179993 PMCID: PMC9526994 DOI: 10.1016/j.fct.2022.113438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
High infection caused by mutations of SARS-CoV-2 calls for new prevention strategy. Ganoderma lucidum known as a superior immunoenhancer exhibits various antiviral effects, whether it can resist SARS-CoV-2 remains unclear. Herein, virtual screening combined with in vitro hACE2 inhibition assays were used to investigate its anti SARS-CoV-2 effect. Potential 54 active components, 80 core targets and 20 crucial pathways were identified by the component-target-pathway network. The binding characters of these components to hACE2 and its complexes with spike protein including omicron variant was analyzed by molecular docking. Lucidenic acid A was selected as the top molecule with high affinity to all receptors by forming hydrogen bonds. Molecular dynamics simulation showed it had good binding stability with the receptor proteins. Finally, in vitro FRET test demonstrated it inhibited the hACE2 activity with IC50 2 μmol/mL. Therefore, lucidenic acid A can prevent the virus invasion by blocking hACE2 binding with SARS-CoV-2.
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Affiliation(s)
- Juan Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - WenTao Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YiFeng Pan
- Hangzhou Xihu District Center for Disease Control and Prevention, Hangzhou, 310030, PR China
| | - HaiShun Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - Liang He
- Zhejiang Provincial Academy of Forestry, Hangzhou, 310000, Zhejiang, China
| | - BingSong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YingQiu Xie
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - XueQian Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China; National Innovation Alliance of Lingzhi and Sanyeqing Industry, Lin'an, 311300, China.
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28
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Purohit P, Sahoo S, Panda M, Sahoo PS, Meher BR. Targeting the DENV NS2B-NS3 protease with active antiviral phytocompounds: structure-based virtual screening, molecular docking and molecular dynamics simulation studies. J Mol Model 2022; 28:365. [PMID: 36274116 PMCID: PMC9589672 DOI: 10.1007/s00894-022-05355-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022]
Abstract
Dengue fever has been a global health concern. Mitigation is a challenging problem due to non-availability of workable treatments. The most difficult objective is to design a perfect anti-dengue agent capable of inhibiting infections caused by all four serotypes. Various tactics have been employed in the past to discover dengue antivirals, including screening of chemical compounds against dengue virus enzymes. The objective of the current study is to investigate phytocompounds as anti-dengue remedies that target the non-structural 2B and non-structural 3 protease (NS2B-NS3pro), a possible therapeutic target for dengue fever. Initially, 300 + antiviral phytocompounds were collected from Duke's phytochemical and ethnobotanical database and 30 phytocompounds with anti-dengue properties were identified from previously reported studies, which were virtually screened against NS2B-NS3pro using molecular docking and toxicity evaluation. The top five most screened ligands were naringin, hesperidin, gossypol, maslinic acid and rhodiolin with binding affinities of - 8.7 kcal/mol, - 8.5 kcal/mol, - 8.5 kcal/mol, - 8.5 kcal/mol and - 8.1 kcal/mol, respectively. The finest docked compounds complexed with NS2B-NS3pro were subjected for molecular dynamics (MD) simulations and binding free energy estimations through molecular mechanics generalized born surface area-based calculations. The results of the study are intriguing in the context of computer-aided screening and the binding affinities of the phytocompounds, proposing maslinic acid (MAS) as a potent bioactive antiviral for the development of phytocompound-based anti-dengue agent.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Sthitaprajna Sahoo
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Partha Sarathi Sahoo
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India.
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29
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Arunachalam K, Sasidharan SP, Yang X. A concise review of mushrooms antiviral and immunomodulatory properties that may combat against COVID-19. FOOD CHEMISTRY ADVANCES 2022; 1:100023. [PMID: 36686330 PMCID: PMC8887958 DOI: 10.1016/j.focha.2022.100023] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 01/25/2023]
Abstract
The World Health Organization (WHO) declared COVID-19 as a pandemic on March 11, 2020, because of its widespread transmission and infection rates. The unique severe disease was found in Wuhan, China, since December 2019, and swiftly spread throughout the world. Natural chemicals derived from herbal medicines and medicinal mushrooms provide a significant resource for the development of novel antiviral drugs. Many natural drugs have been proven to have antiviral properties against a variety of virus strains, such as the coronavirus and the herpes simplex virus (HSV).. In this research, successful dietary treatments for different COVID illnesses were compared to potential of mushroom products in its therapy. In Google Scholar, Science Direct, PubMed, and Scopus, search keywords like COVID, COVID-19, SARS, MERS, mushrooms, and their compounds were utilized. In this review of the literature we foucsed popular mushrooms such as Agaricus subrufescens Peck, Agaricus blazei Murill, Cordyceps sinensis (Berk.) Sacc., Ganoderma lucidum (Curtis.) P. Karst., Grifola frondosa (Dicks.) Gray, Hericium erinaceus (Bull.) Pers., Inonotus obliquus (Arch. Ex Pers.) Pilát., Lentinula edodes (Berk.) Pegler, Pleurotus ostreatus (Jacq.) P. Kumm., Poria cocos F.A. Wolf, and Trametes versicolor (L.) Lloyd.,. Changed forms of β-Glucan seem to have a good impact on viral replication suppression and might be used in future studies. However, the results seems terpenoids, lectins, glycoproteins, lentinan, galactomannan, and polysaccharides from mushrooms are promising prophylactic or therapeutic agents against COVID-19.
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Affiliation(s)
- Karuppusamy Arunachalam
- Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China,University of Chinese Academy of Sciences, Beijing 100049, China,Corresponding authors at: Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | | | - Xuefei Yang
- Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China,University of Chinese Academy of Sciences, Beijing 100049, China,Corresponding authors at: Key Laboratory of Economic Plants and Biotechnology, The Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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30
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Saqallah FG, Abbas MA, Wahab HA. Recent advances in natural products as potential inhibitors of dengue virus with a special emphasis on NS2b/NS3 protease. PHYTOCHEMISTRY 2022; 202:113362. [PMID: 35948138 DOI: 10.1016/j.phytochem.2022.113362] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Dengue virus (DENV) is an arbovirus widespread through tropical and subtropical areas. It is transmitted to humans through Aedes mosquitoes. Infections with DENV can lead to a series of complications, including dengue fever, dengue haemorrhagic fever, or dengue shock syndrome, which might manifest through secondary infections because of a vulnerable immune system. To date, only one tetravalent DENV vaccine is approved to be administered to children whom have been previously DENV-infected and between 9 and 16 years of age. One of the key targets in discovering DENV antiviral agents is the NS2b/NS3 protease. This protease is a crucial enzyme complex for the proteolytic and cleavage activities of the translated polyprotein during DENV life cycle. Several studies were conducted to discover potential antivirals from natural sources or synthetic compounds and peptides. In this review, we describe the recent studies from the past five years dealing with isolated natural products as potential inhibitors of DENV with a greater focus on inhibiting the NS2b/NS3 protease. This review describes recent discoveries in anti-DENV potential of isolated phytochemicals belonging to different groups including fatty acids, glucosides, terpenes and terpenoids, flavonoids, phenolics, chalcones, acetamides, and peptides. Curcumin, quercetin, and myricetin were found to act as non-competitive inhibitors for the NS2b/NS3 protease enzyme. In some studies, the molecular targets of some of these compounds are yet to be identified using in-silico and in-vitro approaches. So far, none of the isolated natural products was tested clinically for the management of DENV infections. The discussed studies demonstrate that natural products are a rich source of potential anti-DENV compounds. However, not all of these compounds were studied for their kinetic molecular mechanism and type of inhibition. In-silico studies provided an ample number of phytochemical hits to be tested experimentally as DENV protease inhibitors. In conclusion, derivatives of these natural products can be designed and synthesised, which could enhance their specificity and efficacy towards the protease. Other sources of natural products, such as fungi, bacterial toxins, marine organisms, and animals, should also be explored towards discovering more potential and effective DENV NS2b/NS3 protease inhibitors.
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Affiliation(s)
- Fadi G Saqallah
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; Discipline of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | - Manal A Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328, Amman, Jordan; Pharmacological and Diagnostic Research Lab, Al-Ahliyya Amman University, 19328, Amman, Jordan.
| | - Habibah A Wahab
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; Discipline of Pharmaceutical Technology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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31
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Liu Y, Yang L, Wang H, Xiong Y. Recent Advances in Antiviral Activities of Triterpenoids. Pharmaceuticals (Basel) 2022; 15:1169. [PMID: 36297280 PMCID: PMC9607549 DOI: 10.3390/ph15101169] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 08/27/2023] Open
Abstract
Triterpenoids, important secondary plant metabolites made up of six isoprene units, are found widely in higher plants and are studied for their structural variety and wide range of bioactivities, including antiviral, antioxidant, anticancer, and anti-inflammatory properties. Numerous studies have demonstrated that different triterpenoids have the potential to behave as potential antiviral agents. The antiviral activities of triterpenoids and their derivatives are summarized in this review, with examples of oleanane, ursane, lupane, dammarane, lanostane, and cycloartane triterpenoids. We concentrated on the tetracyclic and pentacyclic triterpenoids in particular. Furthermore, the particular viral types and possible methods, such as anti-human immunodeficiency virus (HIV), anti-influenza virus, and anti-hepatitis virus, are presented in this article. This review gives an overview and a discussion of triterpenoids as potential antiviral agents.
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Affiliation(s)
- Yue Liu
- Department of Pharmaceutics, Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Liangyu Yang
- Department of Pharmaceutics, Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Hong Wang
- Department of Pharmaceutics, Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Yongai Xiong
- Department of Pharmaceutics, Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
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Oke MA, Afolabi FJ, Oyeleke OO, Kilani TA, Adeosun AR, Olanbiwoninu AA, Adebayo EA. Ganoderma lucidum: Unutilized natural medicine and promising future solution to emerging diseases in Africa. Front Pharmacol 2022; 13:952027. [PMID: 36071846 PMCID: PMC9441938 DOI: 10.3389/fphar.2022.952027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
Ganoderma lucidum is a well-known medicinal mushroom that has been used for the prevention and treatment of different ailments to enhance longevity and health specifically in China, Japan, and Korea. It was known as "God's herb" in ancient China as it was believed to prolong life, enhance the youthful spirit and sustain/preserve vitality. G. lucidum is seldom collected from nature and is substantially cultivated on wood logs and sawdust in plastic bags or bottles to meet the international market demand. Both in vitro and in vivo studies on the copious metabolic activities of G. lucidum have been carried out. Varied groups of chemical compounds including triterpenoids, polysaccharides, proteins, amino acids, nucleosides, alkaloids, steroids, lactones, lectins, fatty acids, and enzymes with potent pharmacological activities have been isolated from the mycelia and fruiting bodies of G. lucidum. Several researchers have reported the abundance and diversification of its biological actions triggered by these chemical compounds. Triterpenoids and polysaccharides of G. lucidum have been reported to possess cytotoxic, hepatoprotective, antihypertensive, hypocholesterolemic, antihistaminic effects, antioxidant, antimicrobial, anti-inflammatory, hypoglycemic antiallergic, neuroprotective, antitumor, immunomodulatory and antiangiogenic activities. Various formulations have been developed, patented, and utilized as nutraceuticals, cosmeceuticals, and pharmaceuticals from G. lucidum extracts and active compounds. Thus, this review presents current updates on emerging infectious diseases and highlights the scope, dynamics, and advances in infectious disease management with a particular focus on Ganoderma lucidum, an unutilized natural medicine as a promising future solution to emerging diseases in Africa. However, details such as the chemical compound and mode of action of each bioactive against different emerging diseases were not discussed in this study.
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Affiliation(s)
- M. A. Oke
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - F. J. Afolabi
- Mushrooms Department, National Biotechnology Development Centre, Ogbomoso, Nigeria
| | - O. O. Oyeleke
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - T. A. Kilani
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - A. R. Adeosun
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
| | - A. A. Olanbiwoninu
- Department of Biological Sciences, Ajayi Crowther University, Oyo, Nigeria
| | - E. A. Adebayo
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Microbiology and Nanobiotechnology Laboratory, LAUTECH, Ogbomoso, Nigeria
- Mushrooms Department, National Biotechnology Development Centre, Ogbomoso, Nigeria
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Cör Andrejč D, Knez Ž, Knez Marevci M. Antioxidant, antibacterial, antitumor, antifungal, antiviral, anti-inflammatory, and nevro-protective activity of Ganoderma lucidum: An overview. Front Pharmacol 2022; 13:934982. [PMID: 35935849 PMCID: PMC9353308 DOI: 10.3389/fphar.2022.934982] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/27/2022] [Indexed: 01/20/2023] Open
Abstract
Ganoderma lucidum is a very medicinal mushroom that has been utilized in Oriental medicine for many years. It has a wide range of pharmacological and therapeutic properties, and has been used for many years as a health promoter. It contains various biologically active compounds that improve the immune system and have antioxidant, antitumor, anti-inflammatory, antifungal, and antimicrobial properties. Active compounds include triterpenoids and polysaccharides, as well as proteins, lipids, phenolics, sterols, etc. In the following review, we summarize briefly their biological activities, such as antioxidant, anti-bacterial, anti-fungal, antitumor, anti-viral, and anti-inflammatory activity. Although Ganoderma has a number of medicinal effects that have been confirmed by the in vitro and in vivo studies summarised in this review, there are some limitations. Clinical trials face mainly a lack of pure constituents. Accurate identification of the compounds obtained is also problematic. In addition, most of the included studies were small, and there were concerns about the methodological quality of each study. Studies have shown that Ganoderma has valuable potential for the prevention and treatment of cancer. In any case, G. lucidum cannot be used as first-line therapy for cancer.
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Affiliation(s)
| | - Željko Knez
- Faculty of Chemistry and Chemical Engineering, Maribor, Slovenia.,Laboratory Faculty of Medicine, Maribor, Slovenia
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Zhang Y, Zhang G, Ling J. Medicinal Fungi with Antiviral Effect. Molecules 2022; 27:molecules27144457. [PMID: 35889330 PMCID: PMC9322162 DOI: 10.3390/molecules27144457] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 02/07/2023] Open
Abstract
Pandemics from various viruses make natural organisms face challenges over and over again. Therefore, new antiviral drugs urgently need to be found to solve this problem. However, drug research and development is a very difficult task, and finding new antiviral compounds is desirable. A range of medicinal fungi such as Ganoderma lucidum and Cordyceps sinensis are widely used all over the world, and they can enhance human immunity and direct anti-virus activities and other aspects to play an antiviral role. Medicinal fungi are used as foods or as food supplements. In this review, the species of medicinal fungi with antiviral activity in recent decades and the mechanism of antiviral components were reviewed from the perspectives of human, animal, and plant viruses to provide a comprehensive theory based on better clinical utilization of medicinal fungi as antiviral agents.
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Affiliation(s)
- Yu Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
- Correspondence: (G.Z.); (J.L.); Tel.: +86-0531-89628200 (G.Z.); +86-0532-58631501 (J.L.)
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Correspondence: (G.Z.); (J.L.); Tel.: +86-0531-89628200 (G.Z.); +86-0532-58631501 (J.L.)
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Katre SG, Asnani AJ, Pratyush K, Sakharkar NG, Bhope AG, Sawarkar KT, Nimbekar VS. Review on development of potential inhibitors of SARS-CoV-2 main protease (M Pro). FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2022; 8:36. [PMID: 35756354 PMCID: PMC9209839 DOI: 10.1186/s43094-022-00423-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background The etiological agent for the coronavirus illness outbreak in 2019-2020 is a novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (COVID-19), whereas coronavirus disease pandemic of 2019 (COVID-19) has compelled the implementation of novel therapeutic options. Main body of the abstract There are currently no targeted therapeutic medicines for this condition, and effective treatment options are quite restricted; however, new therapeutic candidates targeting the viral replication cycle are being investigated. The primary protease of the severe acute respiratory syndrome coronavirus 2 virus is a major target for therapeutic development (MPro). Severe acute respiratory syndrome coronavirus 2, severe acute respiratory syndrome coronavirus, and Middle East respiratory syndrome coronavirus (MERS-CoV) all seem to have a structurally conserved substrate-binding domain that can be used to develop novel protease inhibitors. Short conclusion With the recent publication of the X-ray crystal structure of the severe acute respiratory syndrome coronavirus 2 Mm, virtual and in vitro screening investigations to find MPro inhibitors are fast progressing. The focus of this review is on recent advancements in the quest for small-molecule inhibitors of the severe acute respiratory syndrome coronavirus 2 main protease.
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Affiliation(s)
- Soumya Gulab Katre
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Alpana Jagdish Asnani
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Kumar Pratyush
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | | | - Ashwini Gajanan Bhope
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Kanchan Tekram Sawarkar
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
| | - Vaibhav Santosh Nimbekar
- Department of Pharmaceutical Chemistry, Priyadarshini J L College of Pharmacy, Nagpur, MH 440016 India
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In search of suitable protein targets for anti-malarial and anti-dengue drug discovery. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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El Sheikha AF. Nutritional Profile and Health Benefits of Ganoderma lucidum "Lingzhi, Reishi, or Mannentake" as Functional Foods: Current Scenario and Future Perspectives. Foods 2022; 11:1030. [PMID: 35407117 PMCID: PMC8998036 DOI: 10.3390/foods11071030] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/21/2022] [Accepted: 03/26/2022] [Indexed: 02/07/2023] Open
Abstract
Ganoderma lucidum has a long history of medicinal uses in the Far East countries of more than 2000 years due to its healing properties. Recently, G. lucidum has come under scientific scrutiny to evaluate its content of bioactive components that affect human physiology, and has been exploited for potent components in the pharmacology, nutraceuticals, and cosmetics industries. For instance, evidence is accumulating on the potential of this mushroom species as a promising antiviral medicine for treating many viral diseases, such as dengue virus, enterovirus 71, and recently coronavirus disease of 2019 (COVID-19). Still, more research studies on the biotherapeutic components of G. lucidum are needed to ensure the safety and efficiency of G. lucidum and promote the development of commercial functional foods. This paper provides an extensive overview of the nutraceutical value of Ganoderma lucidum and the development of commercial functional food. Moreover, the geo-origin tracing strategies of this mushroom and its products are discussed, a highly important parameter to ensure product quality and safety. The discussed features will open new avenues and reveal more secrets to widely utilizing this mushroom in many industrial fields; i.e., pharmaceutical and nutritional ones, which will positively reflect the global economy.
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Affiliation(s)
- Aly Farag El Sheikha
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang 330045, China;
- Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON L8S 4K1, Canada
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, 25 University Private, Ottawa, ON K1N 6N5, Canada
- Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang 330045, China
- Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Jiangxi Agricultural University, 1101 Zhimin Road, Nanchang 330045, China
- Department of Food Science and Technology, Faculty of Agriculture, Minufiya University, Shibin El Kom 32511, Egypt
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Kumar S, Paul P, Yadav P, Kaul R, Maitra SS, Jha SK, Chaari A. A multi-targeted approach to identify potential flavonoids against three targets in the SARS-CoV-2 life cycle. Comput Biol Med 2022; 142:105231. [PMID: 35032740 PMCID: PMC8750703 DOI: 10.1016/j.compbiomed.2022.105231] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 02/07/2023]
Abstract
The advent and persistence of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2)-induced Coronavirus Disease (COVID-19) pandemic since December 2019 has created the largest public health emergency in over a century. Despite the administration of multiple vaccines across the globe, there continues to be a lack of approved efficacious non-prophylactic interventions for the disease. Flavonoids are a class of phytochemicals with historically established antiviral, anti-inflammatory and antioxidative properties that are effective against cancers, type 2 diabetes mellitus, and even other human coronaviruses. To identify the most promising bioactive flavonoids against the SARS-CoV-2, this article screened a virtual library of 46 bioactive flavonoids against three promising targets in the SARS-CoV-2 life cycle: human TMPRSS2 protein, 3CLpro, and PLpro. By examining the effects of glycosylation and other structural-activity relationships, the presence of sugar moiety in flavonoids significantly reduces its binding energy. It increases the solubility of flavonoids leading to reduced toxicity and higher bioavailability. Through protein-ligand contact profiling, it was concluded that naringin formed more hydrogen bonds with TMPRSS2 and 3CLpro. In contrast, hesperidin formed a more significant number of hydrogen bonds with PLpro. These observations were complimented by the 100 ns molecular dynamics simulation and binding free energy analysis, which showed a considerable stability of docked bioflavonoids in the active site of SARS-CoV-2 target proteins. Finally, the binding affinity and stability of the selected docked complexes were compared with the reference ligands (camostat for TMPRSS2, GC376 for 3CLpro, and GRL0617 for PLpro) that strongly inhibit their respective SARS-COV-2 targets. Overall analysis revealed that the selected flavonoids could be potential therapeutic agents against SARS-CoV-2. Naringin showed better affinity and stability for TMPRSS2 and 3CLpro, whereas hesperidin showed a better binding relationship and stability for PLpro.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India; Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.
| | - Pradipta Paul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
| | - Pardeep Yadav
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India; Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Ridhima Kaul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
| | - S S Maitra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
| | - Ali Chaari
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144, Qatar.
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Islam MT, Quispe C, Herrera-Bravo J, Sarkar C, Sharma R, Garg N, Fredes LI, Martorell M, Alshehri MM, Sharifi-Rad J, Daştan SD, Calina D, Alsafi R, Alghamdi S, Batiha GES, Cruz-Martins N. Production, Transmission, Pathogenesis, and Control of Dengue Virus: A Literature-Based Undivided Perspective. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4224816. [PMID: 34957305 PMCID: PMC8694986 DOI: 10.1155/2021/4224816] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/11/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022]
Abstract
Dengue remains one of the most serious and widespread mosquito-borne viral infections in human beings, with serious health problems or even death. About 50 to 100 million people are newly infected annually, with almost 2.5 billion people living at risk and resulting in 20,000 deaths. Dengue virus infection is especially transmitted through bites of Aedes mosquitos, hugely spread in tropical and subtropical environments, mostly found in urban and semiurban areas. Unfortunately, there is no particular therapeutic approach, but prevention, adequate consciousness, detection at earlier stage of viral infection, and appropriate medical care can lower the fatality rates. This review offers a comprehensive view of production, transmission, pathogenesis, and control measures of the dengue virus and its vectors.
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Affiliation(s)
- Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj (Dhaka)8100, Bangladesh
| | - Cristina Quispe
- Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Jesús Herrera-Bravo
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Chile
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Chandan Sarkar
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj (Dhaka)8100, Bangladesh
| | - Rohit Sharma
- Department of Rasa Shastra & Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Neha Garg
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | | | - Miquel Martorell
- Department of Nutrition and Dietetics, Faculty of Pharmacy, and Centre for Healthy Living, University of Concepción, 4070386 Concepción, Chile
- Universidad de Concepción, Unidad de Desarrollo Tecnológico, UDT, Concepción 4070386, Chile
| | - Mohammed M. Alshehri
- Pharmaceutical Care Department, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | | | - Sevgi Durna Daştan
- Department of Biology, Faculty of Science, Sivas Cumhuriyet University, 58140 Sivas, Turkey
- Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, 58140 Sivas, Turkey
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Radi Alsafi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Institute of Research and Advanced Training in Health Sciences and Technologies (CESPU), Rua Central de Gandra, 1317, 4585-116 Gandra PRD, Portugal
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Roney M, Huq AKMM, Rullah K, Hamid HA, Imran S, Islam MA, Mohd Aluwi MFF. Virtual Screening-Based Identification of Potent DENV-3 RdRp Protease Inhibitors via In-House Usnic Acid Derivative Database. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Dengue virus (DENV) is the causative agent of dengue fever, dengue hemorrhagic disease and dengue shock syndrome (DSS), transmitted predominantly in tropical and subtropical regions by Aedes aegypti. It infects millions of people and causes thousands of deaths each year, but there is no antiviral drug against DENV. Usnic acid lately piqued the interest of researchers for extraordinary biological characteristics, including antiviral activity. Based on high larvicidal activities against Aedes aegypti, this study aims to search usnic acid derivatives as novel anti-DENV agents through a combination of ligand-based and pharmacophore-based virtual screening. One hundred and sixteen (116) usnic acid derivatives were obtained from a database of 428 in-house usnic acid derivatives through pharmacophore filtering steps. Subsequent docking simulation on DENV-3 NS-5 RdRp afforded 41 compounds with a strong binding affinity towards the enzyme. The pharmacokinetics and drug likeness prediction resulted in seven hit compounds, which eventually undergo cytochrome P450 enzyme screening to obtain the lead compound, labelled as 362. In addition, molecular dynamic (MD) simulation of lead compound 362 was performed to verify the stability of the docked complex and the binding posture acquired in docking experiments. Overall, the lead compounds have shown a high fit value of pharmacophore, strong binding affinity towards RdRp enzyme, good pharmacokinetics, and drug likeness properties. The discovery of a new usnic acid derivative as a novel anti-DENV agent targeting RdRp could lead to further drug development and optimization to treat dengue.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - AKM Moyeenul Huq
- Department of Pharmacy, School of Medicine, University of Asia Pacific, 74/A, Green Road, Dhaka 1205, Bangladesh
| | - Kamal Rullah
- Kulliyyah of Pharmacy, International Islamic University Malaysia (IIUM), Jalan Sultan Ahmad Shah, 25200 Kuantan, Pahang, Malaysia
| | - Hazrulrizawati Abd Hamid
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery, UiTM Selangor, Kampus Puncak Alam, 42300 Bandar Puncak Alam, Malaysia
| | - Md. Alimul Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University Mymensingh 2202, Bangladesh
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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Biosynthesis and regulation of terpenoids from basidiomycetes: exploration of new research. AMB Express 2021; 11:150. [PMID: 34779947 PMCID: PMC8594250 DOI: 10.1186/s13568-021-01304-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/16/2021] [Indexed: 12/15/2022] Open
Abstract
Basidiomycetes, also known as club fungi, consist of a specific group of fungi. Basidiomycetes produce a large number of secondary metabolites, of which sesquiterpenoids, diterpenoids and triterpenoids are the primary components. However, these terpenoids tend to be present in low amounts, which makes it difficult to meet application requirements. Terpenoid biosynthesis improves the quantity of these secondary metabolites. However, current understanding of the biosynthetic mechanism of terpenoids in basidiomycetes is insufficient. Therefore, this article reviews the latest research on the biosynthesis of terpenoids in basidiomycetes and summarizes the CYP450 involved in the biosynthesis of terpenoids in basidiomycetes. We also propose opportunities and challenges for chassis microbial heterologous production of terpenoids in basidiomycetes and provide a reference basis for the better development of basidiomycete engineering.
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Arshia AH, Shadravan S, Solhjoo A, Sakhteman A, Sami A. De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations. Comput Biol Med 2021; 139:104967. [PMID: 34739968 PMCID: PMC8545757 DOI: 10.1016/j.compbiomed.2021.104967] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/15/2022]
Abstract
The main protease of SARS-CoV-2 is a critical target for the design and development of antiviral drugs. 2.5 M compounds were used in this study to train an LSTM generative network via transfer learning in order to identify the four best candidates capable of inhibiting the main proteases in SARS-CoV-2. The network was fine-tuned over ten generations, with each generation resulting in higher binding affinity scores. The binding affinities and interactions between the selected candidates and the SARS-CoV-2 main protease are predicted using a molecular docking simulation using AutoDock Vina. The compounds selected have a strong interaction with the key MET 165 and Cys145 residues. Molecular dynamics (MD) simulations were run for 150ns to validate the docking results on the top four ligands. Additionally, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and hydrogen bond analysis strongly support these findings. Furthermore, the MM-PBSA free energy calculations revealed that these chemical molecules have stable and favorable energies, resulting in a strong binding with Mpro's binding site. This study's extensive computational and statistical analyses indicate that the selected candidates may be used as potential inhibitors against the SARS-CoV-2 in-silico environment. However, additional in-vitro, in-vivo, and clinical trials are required to demonstrate their true efficacy.
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Affiliation(s)
- Amir Hossein Arshia
- CSE and IT Department; School of Electrical Engineering and Computer; Shiraz University, Shiraz, Iran
| | - Shayan Shadravan
- CSE and IT Department; School of Electrical Engineering and Computer; Shiraz University, Shiraz, Iran
| | - Aida Solhjoo
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ashkan Sami
- CSE and IT Department; School of Electrical Engineering and Computer; Shiraz University, Shiraz, Iran.
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Murtuja S, Shilkar D, Sarkar B, Sinha BN, Jayaprakash V. A short survey of dengue protease inhibitor development in the past 6 years (2015-2020) with an emphasis on similarities between DENV and SARS-CoV-2 proteases. Bioorg Med Chem 2021; 49:116415. [PMID: 34601454 PMCID: PMC8450225 DOI: 10.1016/j.bmc.2021.116415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/06/2021] [Accepted: 09/11/2021] [Indexed: 11/26/2022]
Abstract
Dengue remains a disease of significant concern, responsible for nearly half of all arthropod-borne disease cases across the globe. Due to the lack of potent and targeted therapeutics, palliative treatment and the adoption of preventive measures remain the only available options. Compounding the problem further, the failure of the only dengue vaccine, Dengvaxia®, also delivered a significant blow to any hopes for the treatment of dengue fever. However, the success of Human Immuno-deficiency Virus (HIV) and Hepatitis C Virus (HCV) protease inhibitors in the past have continued to encourage researchers to investigate other viral protease targets. Dengue virus (DENV) NS2B-NS3 protease is an attractive target partly due to its role in polyprotein processing and also for being the most conserved domain in the viral genome. During the early days of the COVID-19 pandemic, a few cases of Dengue-COVID 19 co-infection were reported. In this review, we compared the substrate-peptide residue preferences and the residues lining the sub-pockets of the proteases of these two viruses and analyzed the significance of this similarity. Also, we attempted to abridge the developments in anti-dengue drug discovery in the last six years (2015-2020), focusing on critical discoveries that influenced the research.
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Affiliation(s)
- Sheikh Murtuja
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH), India
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH), India
| | - Biswatrish Sarkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH), India
| | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH), India
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH), India.
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Mechanistic insights into the Japanese encephalitis virus RNA dependent RNA polymerase protein inhibition by bioflavonoids from Azadirachta indica. Sci Rep 2021; 11:18125. [PMID: 34518560 PMCID: PMC8437980 DOI: 10.1038/s41598-021-96917-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Japanese encephalitis (JE) virus is a flavivirus causing encephalitis causing neurological damage. RNA-dependent-RNA-polymerase (RdRp) is responsible for genome replication making it excellent anti-viral target. In this study, the crystal structure of JE RdRp (jRdRp) and bioflavonoids reported in Azadirachta indica were retrieved from specific databases. Structure-based virtual screening was employed using MTiOpenScreen server and top four compounds selected with the most negative docking scores. Conformations were redocked using AutoDock Vina; these complexes showed mechanistic interactions with Arg474, Gly605, Asp668, and Trp800 residues in the active site of jRdRp, i.e., guanosine-5′-triphosphate. Furthermore, 100 ns classical molecular dynamics simulation and binding free energy calculation showed stability of docked bioflavonoids in the active jRdRp pocket and significant contribution of van-der-Waals interactions for docked complex stability during simulation. Therefore, this study predicted the anti-viral activity of Gedunin, Nimbolide, Ohchinin acetate, and Kulactone against jRdRp and can be considered for further antiviral drug development.
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Kaewnarin K, Limjiasahapong S, Jariyasopit N, Anekthanakul K, Kurilung A, Wong SCC, Sirivatanauksorn Y, Visessanguan W, Khoomrung S. High-Resolution QTOF-MRM for Highly Accurate Identification and Quantification of Trace Levels of Triterpenoids in Ganoderma lucidum Mycelium. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2451-2462. [PMID: 34412475 DOI: 10.1021/jasms.1c00175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The accurate quantification of triterpenoids in Ganoderma lucidum mushroom in the mycelium stage is challenging due to their low concentrations, interference from other possible isomers, and the complex matrix. Here, a high-resolution quadrupole-time-of-flight mass spectrometry "multiple reaction monitoring" with target enhancement (HR-QTOF-MRM) method was developed to quantify seven target triterpenoids in G. lucidum. The performance of this method was compared against an optimized QQQ-MRM method. The HR-QTOF-MRM was shown to be capable of distinguishing target triterpenoids from interferent peaks in the presence of matrices. The HR-QTOF-MRM LOD and LLOQ values were found to be one to two times lower than those derived from the QQQ-MRM method. Intraday and interday variabilities of the HR-QTOF-MRM demonstrated better reproducibility than the QQQ-MRM. In addition, excellent recoveries of the analytes ranging from 80 to 117% were achieved. Spiking experiments were carried out to verify and compare the quantitative accuracy of the two methods. The HR-QTOF-MRM method provided better percent accuracy, ranging from 84% to 99% (<3% RSD), compared with the range of 69 to 114% (<4%RSD) given by the QQQ-MRM method. These results demonstrate that the new HR-QTOF-MRM mode is able to improve sensitivity, reproducibility, and accuracy of trace level analysis of triterpenoids in the complex biological samples. The triterpenoid concentrations were in the range of nondetect to 0.06-6.72 mg/g of dried weight in fruiting body and to 0.0009-0.01 mg/g of dried weight in mycelium.
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Affiliation(s)
- Khwanta Kaewnarin
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Suphitcha Limjiasahapong
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Narumol Jariyasopit
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Krittima Anekthanakul
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Alongkorn Kurilung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | | | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani 12120, Thailand
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10700, Thailand
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Sisakht M, Solhjoo A, Mahmoodzadeh A, Fathalipour M, Kabiri M, Sakhteman A. Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19. Comput Biol Med 2021; 136:104686. [PMID: 34340125 PMCID: PMC8319042 DOI: 10.1016/j.compbiomed.2021.104686] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023]
Abstract
The main protease of SARS-CoV-2 is one of the key targets to develop and design antiviral drugs. There is no general agreement on the use of non-steroidal anti-inflammatory drugs (NSAIDs) in COVID-19. In this study, we investigated NSAIDs as potential inhibitors for chymotrypsin-like protease (3CLpro) and the main protease of the SARS-CoV-2 to find out the best candidates, which can act as potent inhibitors against the main protease. We also predicted the effect of NSAIDs on the arachidonic pathway and evaluated the hepatotoxicity of the compounds using systems biology techniques. Molecular docking was conducted via AutoDock Vina to estimate the interactions and binding affinities between selected NSAIDs and the main protease. Molecular docking results showed the presence of 10 NSAIDs based on lower binding energy (kcal/mol) toward the 3CLpro inhibition site compared to the co-crystal native ligand Inhibitor N3 (-6.6 kcal/mol). To validate the docking results, molecular dynamic (MD) simulations on the top inhibitor, Talniflumate, were performed. To obtain differentially-expressed genes under the 27 NSAIDs perturbations, we utilized the L1000 final Z-scores from the NCBI GEO repository (GSE92742). The obtained dataset included gene expression profiling signatures for 27 NSAIDs. The hepatotoxicity of NSAIDs was studied by systems biology modeling of Disturbed Metabolic Pathways. This study highlights the new application of NSAIDs as anti-viral drugs used against COVID-19. NSAIDs may also attenuate the cytokine storm through the downregulation of inflammatory mediators in the arachidonic acid pathway.
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Affiliation(s)
- Mohsen Sisakht
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Mahmoodzadeh
- Feinberg Cardiovascular Research Institute, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Mohammad Fathalipour
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Endocrinology and Metabolic Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Maryam Kabiri
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
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Differences in Antioxidants, Polyphenols, Protein Digestibility and Nutritional Profile between Ganoderma lingzhi from Industrial Crops in Asia and Ganoderma lucidum from Cultivation and Iberian Origin. Foods 2021; 10:foods10081750. [PMID: 34441528 PMCID: PMC8394434 DOI: 10.3390/foods10081750] [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: 06/26/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Carpophores of Ganoderma lingzhi (GZ) from industrial crops in China were analysed and compared with carpophores of three Iberian strains of cultivated Ganoderma lucidum (GL) (Aveiro, Madrid, Palencia) previously genetically characterized. The genetic determination of all the fungi in the study coincided with the identification provided by the companies and entities that supplied the samples. Cultivation time ranged between 107 and 141 days. The analysis of total phenol content showed to be 56.8% higher for GL from Palencia than for GZ. Intraspecific variation was a maximum of 56% from GL. The content of antioxidants, both intraspecific and interspecific, was found to be strain-dependent with a maximum variation of 78.5%. The nutritional analysis shows that there are differences in dietary fiber, protein, ash and sodium content between GL and GZ. In fatty acids analysis, only trans fatty acids showed significant differences, being higher in GL. Protein profile and digestibility of GZ and GL-Madrid mushroom proteins were evaluated by digestion with simulated gastric fluid and were different. The two species were perfectly differentiated according to their protein profile. These results should be considered for nutritional and industrial applications.
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Ganoderma lucidum: A potential source to surmount viral infections through β-glucans immunomodulatory and triterpenoids antiviral properties. Int J Biol Macromol 2021; 187:769-779. [PMID: 34197853 DOI: 10.1016/j.ijbiomac.2021.06.122] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/11/2022]
Abstract
Ganoderma lucidum (G. lucidum) polysaccharides and triterpenoids are the major bioactive compounds and have been used as traditional medicine for ancient times. Massive demands of G. lucidum have fascinated the researchers towards its application as functional food, nutraceutical and modern medicine owing to wide range of application in various diseases include immunomodulators, anticancer, antiviral, antioxidant, cardioprotective, hepatoprotective. G. lucidum polysaccharides exhibit immunomodulatory properties through boosting the action of antigen-presenting cells, mononuclear phagocyte system, along with humoral and cellular immunity. β-Glucans isolated from G. lucidum are anticipated to produce an immune response through pathogen associated molecular patterns (PAMPs). β-Glucans after binding with dectin-1 receptor present on different cells include macrophages, monocytes, dendritic cells and neutrophils produce signal transduction that lead to trigger the mitogen-activated protein kinases (MAPKs), T cells and Nuclear factor-κB (NF-κB) that refer to cytokines production and contributing to immune response. While triterpenoids produce antiviral effects through inhibiting various enzymes like neuraminidase, HIV-protease, DENV2 NS2B-NS3 protease and HSV multiplication. Polysaccharides and triterpenoids adjunct to other drugs exhibit potential action in prevention and treatment of various diseases. Immunomodulators and antiviral properties of this mushroom could be a potential source to overcome this current pandemic outbreak.
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Facile Synthesis and In Vitro Activity of N-Substituted 1,2-Benzisothiazol-3(2 H)-ones against Dengue Virus NS2BNS3 Protease. Pathogens 2021; 10:pathogens10040464. [PMID: 33921368 PMCID: PMC8070447 DOI: 10.3390/pathogens10040464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/02/2022] Open
Abstract
Several new N-substituted 1,2-benzisothiazol-3(2H)-ones (BITs) were synthesised through a facile synthetic route for testing their anti-dengue protease inhibition. Contrary to the conventional multistep synthesis, we achieved structurally diverse BITs with excellent yields using a two-step, one-pot reaction strategy. All the synthesised compounds were prescreened for drug-like properties using the online Swiss Absorption, Distribution, Metabolism and Elimination (SwissADME) model, indicating their favourable pharmaceutical properties. Thus, the synthesised BITs were tested for inhibitory activity against the recombinant dengue virus serotype-2 (DENV-2) NS2BNS3 protease. Dose–response experiments and computational docking analyses revealed that several BITs bind to the protease in the vicinity of the catalytic triad with IC50 values in the micromolar range. The DENV2 infection assay showed that two BITs, 2-(2-chlorophenyl)benzo[d]isothiazol-3(2H)-one and 2-(2,6-dichlorophenyl)benzo[d]isothiazol-3(2H)-one, could suppress DENV replication and virus infectivity. These results indicate the potential of BITs for developing new anti-dengue therapeutics.
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Christy MP, Uekusa Y, Gerwick L, Gerwick WH. Natural Products with Potential to Treat RNA Virus Pathogens Including SARS-CoV-2. JOURNAL OF NATURAL PRODUCTS 2021; 84:161-182. [PMID: 33352046 PMCID: PMC7771248 DOI: 10.1021/acs.jnatprod.0c00968] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Indexed: 05/03/2023]
Abstract
Three families of RNA viruses, the Coronaviridae, Flaviviridae, and Filoviridae, collectively have great potential to cause epidemic disease in human populations. The current SARS-CoV-2 (Coronaviridae) responsible for the COVID-19 pandemic underscores the lack of effective medications currently available to treat these classes of viral pathogens. Similarly, the Flaviviridae, which includes such viruses as Dengue, West Nile, and Zika, and the Filoviridae, with the Ebola-type viruses, as examples, all lack effective therapeutics. In this review, we present fundamental information concerning the biology of these three virus families, including their genomic makeup, mode of infection of human cells, and key proteins that may offer targeted therapies. Further, we present the natural products and their derivatives that have documented activities to these viral and host proteins, offering hope for future mechanism-based antiviral therapeutics. By arranging these potential protein targets and their natural product inhibitors by target type across these three families of virus, new insights are developed, and crossover treatment strategies are suggested. Hence, natural products, as is the case for other therapeutic areas, continue to be a promising source of structurally diverse new anti-RNA virus therapeutics.
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Affiliation(s)
- Mitchell P. Christy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Yoshinori Uekusa
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
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