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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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Ahmad S, Zahiruddin S, Parveen B, Basist P, Parveen A, Gaurav, Parveen R, Ahmad M. Indian Medicinal Plants and Formulations and Their Potential Against COVID-19-Preclinical and Clinical Research. Front Pharmacol 2021; 11:578970. [PMID: 33737875 PMCID: PMC7962606 DOI: 10.3389/fphar.2020.578970] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/29/2020] [Indexed: 12/11/2022] Open
Abstract
The cases of COVID-19 are still increasing day-by-day worldwide, even after a year of its first occurrence in Wuhan city of China. The spreading of SARS-CoV-2 infection is very fast and different from other SARS-CoV infections possibly due to structural differences in S proteins. The patients with severe diseases may die due to acute respiratory distress syndrome (ARDS) caused by systemic inflammatory reactions due to the excessive release of pro-inflammatory cytokines and chemokines by the immune effector cells. In India too, it is spreading very rapidly, although the case fatality rate is below 1.50% (https://www.statista.com), which is markedly less than in other countries, despite the dense population and minimal health infrastructure in rural areas. This may be due to the routine use of many immunomodulator medicinal plants and traditional AYUSH formulations by the Indian people. This communication reviews the AYUSH recommended formulations and their ingredients, routinely used medicinal plants and formulations by Indian population as well as other promising Indian medicinal plants, which can be tested against COVID-19. Special emphasis is placed on Indian medicinal plants reported for antiviral, immunomodulatory and anti-allergic/anti-inflammatory activities and they are categorized for prioritization in research on the basis of earlier reports. The traditional AYUSH medicines currently under clinical trials against COVID-19 are also discussed as well as furtherance of pre-clinical and clinical testing of the potential traditional medicines against COVID-19 and SARS-CoV-2. The results of the clinical studies on AYUSH drugs will guide the policymakers from the AYUSH systems of medicines to maneuver their policies for public health, provide information to the global scientific community and could form a platform for collaborative studies at national and global levels. It is thereby suggested that promising AYUSH formulations and Indian medicinal plants must be investigated on a priority basis to solve the current crisis.
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Affiliation(s)
- Sayeed Ahmad
- Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Deemed University), New Delhi, India
| | - Sultan Zahiruddin
- Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Deemed University), New Delhi, India
| | - Bushra Parveen
- Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Deemed University), New Delhi, India
| | - Parakh Basist
- Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Deemed University), New Delhi, India
| | - Abida Parveen
- Centre for Translational and Clinical Research, Jamia Hamdard (Deemed University), New Delhi, India
| | - Gaurav
- Bioactive Natural Product Laboratory, Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard (Deemed University), New Delhi, India
| | - Rabea Parveen
- Department of Biosciences, Jamia Millia Islamia (Central University), New Delhi, India
| | - Minhaj Ahmad
- Department of Surgery, School of Unani Medical Education and Research, Jamia Hamdard (Deemed University), New Delhi, India
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Bhowmick S, Alissa SA, Wabaidur SM, Chikhale RV, Islam MA. Structure-guided screening of chemical database to identify NS3-NS2B inhibitors for effective therapeutic application in dengue infection. J Mol Recognit 2020; 33:e2838. [PMID: 32060998 DOI: 10.1002/jmr.2838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/01/2020] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
Abstract
Dengue infection is the most common arthropod-borne disease caused by dengue viruses, predominantly affecting millions of human beings annually. To find out promising chemical entities for therapeutic application in Dengue, in the current research, a multi-step virtual screening effort was conceived to screen out the entire "screening library" of the Asinex database. Initially, through "Lipinski rule of five" filtration criterion almost 0.6 million compounds were collected and docked with NS3-NS2B protein. Thereby, the chemical space was reduced to about 3500 compounds through the analysis of binding affinity obtained from molecular docking study in AutoDock Vina. Further, the "Virtual Screening Workflow" (VSW) utility of Schrödinger suite was used, which follows a stepwise multiple docking programs such as - high-throughput virtual screening (HTVS), standard precision (SP), and extra precision (XP) docking, and in postprocessing analysis the MM-GBSA based free binding energy calculation. Finally, five potent molecules were proposed as potential inhibitors for the dengue NS3-NS2B protein based on the investigation of molecular interactions map and protein-ligand fingerprint analyses. Different pharmacokinetics and drug-likeness parameters were also checked, which favour the potentiality of selected molecules for being drug-like candidates. The molecular dynamics (MD) simulation analyses of protein-ligand complexes were explained that NS3-NS2B bound with proposed molecules quite stable in dynamic states as observed from the root means square deviation (RMSD) and root means square fluctuation (RMSF) parameters. The binding free energy was calculated using MM-GBSA method from the MD simulation trajectories revealed that all proposed molecules possess such a strong binding affinity towards the dengue NS3-NS2B protein. Therefore, proposed molecules may be potential chemical components for effective inhibition of dengue NS3-NS2B protein subjected to experimental validation.
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Affiliation(s)
- Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, Kolkata, India
| | - Siham A Alissa
- Chemistry Department, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,School of Health Sciences, University of Kwazulu-Natal, Westville Campus, Durban, South Africa.,Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Trujillo-Correa AI, Quintero-Gil DC, Diaz-Castillo F, Quiñones W, Robledo SM, Martinez-Gutierrez M. In vitro and in silico anti-dengue activity of compounds obtained from Psidium guajava through bioprospecting. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:298. [PMID: 31694638 PMCID: PMC6836419 DOI: 10.1186/s12906-019-2695-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 09/25/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND For decades, bioprospecting has proven to be useful for the identification of compounds with pharmacological potential. Considering the great diversity of Colombian plants and the serious worldwide public health problem of dengue-a disease caused by the dengue virus (DENV)-in the present study, we evaluated the anti-DENV effects of 12 ethanolic extracts derived from plants collected in the Colombian Caribbean coast, and 5 fractions and 5 compounds derived from Psidium guajava. METHODS The cytotoxicity and antiviral effect of 12 ethanolic extracts derived from plants collected in the Colombian Caribbean coast was evaluated in epithelial VERO cells. Five fractions were obtained by open column chromatography from the ethanolic extract with the highest selectivity index (SI) (derived from P. guajava, SI: 128.2). From the fraction with the highest selectivity (Pg-YP-I-22C, SI: 35.5), five compounds were identified by one- and two-dimensional nuclear magnetic resonance spectroscopy. The antiviral effect in vitro of the fractions and compounds was evaluated by different experimental strategies (Pre- and post-treatment) using non-toxic concentrations calculated by MTT method. The DENV inhibition was evaluated by plate focus assay. The results were analyzed by means of statistical analysis using Student's t-test. Finally the antiviral effect in Silico was evaluated by molecular docking. RESULTS In vitro evaluation of these compounds showed that three of them (gallic acid, quercetin, and catechin) were promising antivirals as they inhibit the production of infectious viral particles via different experimental strategies, with the best antiviral being catechin (100% inhibition with a pre-treatment strategy and 91.8% with a post-treatment strategy). When testing the interactions of these compounds with the viral envelope protein in silico by docking, only naringin and hesperidin had better scores than the theoretical threshold of - 7.0 kcal/mol (- 8.0 kcal/mol and - 8.2 kcal/mol, respectively). All ligands tested except gallic acid showed higher affinity to the NS5 protein than the theoretical threshold. CONCLUSION Even though bioprospecting has recently been replaced by more targeted tools for identifying compounds with pharmacological potential, our results show it is still useful for this purpose. Additionally, combining in vitro and in silico evaluations allowed us to identify promising antivirals as well as their possible mechanisms of action.
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Neelawala D, Rajapakse S, Kumbukgolla WW. Potential of medicinal plants to treat dengue. INTERNATIONAL JOURNAL OF ONE HEALTH 2019. [DOI: 10.14202/ijoh.2019.86-91] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Dengue is a major public health challenge worldwide, particularly in tropical areas. Nearly 390 million infections and 22,000 deaths occur every year. At present, there are no specific therapeutics available to treat dengue; however, possible treatment procedures are explained in the traditional medical systems (TMSs), such as Sri Lankan TMS, Indian Ayurvedic, Unani, and Siddha TMS. In these TMSs, medicinal plants have been used in several ways against dengue, such as virocides, larvicides, and mosquito repellents. Therefore, medicinal plants inherit biologically active compounds/lead compounds that are yet to be identified chemically and physiologically. Herein, we discuss the possible applications of crude plant extracts and isolated phytochemicals from medicinal plants such as quercetin, sulfated galactomannans, flavonoids, and glabranine in controlling dengue. Moreover, medicinal plant-based therapeutics can be safer, cost-effective, and non-toxic. Therefore, this paper reviews the medicinal plants that are used in TMSs to manage dengue, the phytochemicals they contain, and mode of action of these phytochemicals such as virocides, larvicides, and mosquito repellents.
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Affiliation(s)
- Dulanjalee Neelawala
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Anuradhapura 50000, Sri Lanka
| | - Sanjaya Rajapakse
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Anuradhapura 50000, Sri Lanka
| | - Wikum Widuranga Kumbukgolla
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Anuradhapura 50000, Sri Lanka
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Jindapunnapat K, Reetz ND, MacDonald MH, Bhagavathy G, Chinnasri B, Soonthornchareonnon N, Sasnarukkit A, Chauhan KR, Chitwood DJ, Meyer SLF. Activity of Vetiver Extracts and Essential Oil against Meloidogyne incognita. J Nematol 2018; 50:147-162. [PMID: 30451435 DOI: 10.21307/jofnem-2018-008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Vetiver, a nonhost grass for certain nematodes, was studied for the production of compounds active against the southern root-knot nematode, Meloidogyne incognita . In laboratory assays studying the effects on second-stage juvenile (J2) activity and viability, crude vetiver root and shoot extracts were nematotoxic, resulting in 40% to 70% J2 mortality, and were also repellent to J2. Vetiver oil did not exhibit activity against J2 in these assays. Gas chromatography-mass spectrometry analyses of three crude vetiver root ethanol extracts and a commercial vetiver oil determined that two of the major components in each sample were the sesquiterpene acid 3,3,8,8-tetramethyltricyclo[5.1.0.0(2,4)]oct-5-ene-5-propanoic acid and the sesquiterpene alcohol 6-isopropenyl-4,8a-dimethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-2-ol. The acid was present in higher amounts in the extracts than in the oil. These studies demonstrating nematotoxicity and repellency of vetiver-derived compounds to M. incognita suggest that plant chemistry plays a role in the nonhost status of vetiver to root-knot nematodes, and that the chemical constituents of vetiver may be useful for suppressing nematode populations in the soil.
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Affiliation(s)
- Kansiree Jindapunnapat
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand ; Center for Advanced Studies for Agriculture and Food, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand (CASAF, NRU-KU, Thailand) ; USDA, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705
| | - Nathan D Reetz
- USDA, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705
| | - Margaret H MacDonald
- USDA, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705
| | - Ganga Bhagavathy
- USDA, ARS, Invasive Insect Biocontrol and Behavior Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705
| | - Buncha Chinnasri
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | | | - Anongnuch Sasnarukkit
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Kamlesh R Chauhan
- USDA, ARS, Invasive Insect Biocontrol and Behavior Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705
| | - David J Chitwood
- USDA, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705
| | - Susan L F Meyer
- USDA, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Northeast Area, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705
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