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Kothapalli Y, Jones RA, Chu CK, Singh US. Synthesis of Fluorinated Nucleosides/Nucleotides and Their Antiviral Properties. Molecules 2024; 29:2390. [PMID: 38792251 PMCID: PMC11124531 DOI: 10.3390/molecules29102390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The FDA has approved several drugs based on the fluorinated nucleoside pharmacophore, and numerous drugs are currently in clinical trials. Fluorine-containing nucleos(t)ides offer significant antiviral and anticancer activity. The insertion of a fluorine atom, either in the base or sugar of nucleos(t)ides, alters its electronic and steric parameters and transforms the lipophilicity, pharmacodynamic, and pharmacokinetic properties of these moieties. The fluorine atom restricts the oxidative metabolism of drugs and provides enzymatic metabolic stability towards the glycosidic bond of the nucleos(t)ide. The incorporation of fluorine also demonstrates additional hydrogen bonding interactions in receptors with enhanced biological profiles. The present article discusses the synthetic methodology and antiviral activities of FDA-approved drugs and ongoing fluoro-containing nucleos(t)ide drug candidates in clinical trials.
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Affiliation(s)
| | | | - Chung K. Chu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (Y.K.); (R.A.J.)
| | - Uma S. Singh
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (Y.K.); (R.A.J.)
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2
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Alhazmi AY, Khan FR, Rehman ZU, Hazazi A, Alotaibi BS, Alharthi NS, Alhuthali HM, Aba Alkhayl FF, Alshehri FF, Alkhoshaiban A, Al-Otaibi F. Structural and energetic analysis of NS5 protein inhibition by small molecules in Japanese encephalitis virus using machine learning and steered molecular dynamics approach. J Biomol Struct Dyn 2024:1-18. [PMID: 38407246 DOI: 10.1080/07391102.2024.2316767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
One of the viral diseases that affect millions of people around the world, particularly in developing countries, is Japanese encephalitis (JE). In this study, the conserved protein of this virus, that is, non-structural protein 5 (NS5), was used as a target protein for this study, and a compound library of 749 antiviral molecules was screened against NS5. The current study employed machine learning-based virtual screening combined with molecular docking. Here, three hits (24360, 123519051 and 213039) had lower binding energies (< -8 kcal/mol) than the control, S-Adenosyl-L-homocysteine (SAH). All the compounds showed significant H-bond interactions with functional residues, which were also observed by the control. Molecular dynamics simulation, MM/GBSA for binding free energy analysis, principal component analysis and free energy landscape were also performed to study the stability of the complex formation. All three compounds had similar root mean square deviation trends, which were comparable to the control, SAH. Post-MD, the 123519051-receptor complex had the highest number of H-bonds (4 to 5) after the control, out of which three exhibited the highest percentage occupancy (50%, 24% and 79%). Both docking and MD, 123519051 showed an H-bond with the residue Gly111, which was also found for the control-protein complex. 123519051 showed the lowest binding free energy with ΔGbind of -89 kJ/mol. Steered molecular dynamics depicted that 123519051 had the maximum magnitude of dissociation (1436.43 kJ/mol/nm), which was more than the control, validating its stable complex formation. This study concluded that 123519051 is a binder and could inhibit the protein NS5 of JE.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdulfattah Y Alhazmi
- Pharmaceutical Practices Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences - AlQuwayiyah, Shaqra University, Saudi Arabia
| | - Zia Ur Rehman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences - AlQuwayiyah, Shaqra University, Saudi Arabia
| | - Nahed S Alharthi
- Department of Medical Laboratory. College of Applied Medical Sciences in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudia Arabia
| | - Hayaa M Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Faris F Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faez Falah Alshehri
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | | | - Faisal Al-Otaibi
- Department of Pharmacy Practice, College of Pharmacy, Shaqra University, Saudi Arabia
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Malik M, Vijayan P, Jagannath DK, Mishra RK, Lakshminarasimhan A. Sofosbuvir and its tri-phosphate metabolite inhibit the RNA-dependent RNA polymerase activity of non-structural protein 5 from the Kyasanur forest disease virus. Biochem Biophys Res Commun 2023; 641:50-56. [PMID: 36521285 DOI: 10.1016/j.bbrc.2022.12.023] [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: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Kyasanur forest disease is a neglected zoonotic disease caused by a single-stranded RNA-based flavivirus, the incidence of which was first recorded in 1957 in the Southern part of India. Kyasanur forest disease virus is transmitted to monkeys and humans through the infected tick bite of Haemophysalis spinigera. Kyasanur forest disease is a febrile illness, which in severe cases, results in neurological complications leading to mortality. The current treatment regimens are symptomatic and supportive, and no targeted therapies are available for this disease. In this study, we evaluated the ability of FDA-approved drugs sofosbuvir (and its active metabolite) and Dasabuvir to inhibit the RNA-dependent RNA polymerase activity of NS5 protein from the Kyasanur forest disease virus. NS5 protein containing the N-terminal methyl transferase domain and C-terminal RNA-dependent RNA polymerase domain was expressed in Escherichia coli, and RNA-dependent RNA polymerase activity was demonstrated with the purified protein. The RNA-dependent RNA polymerase assay conditions were optimized, followed by the determination of apparent Km,ATP to validate the enzyme preparation. Half maximal-inhibitory concentrations against RNA-dependent RNA polymerase activity were determined for Sofosbuvir and its active metabolite. Dasabuvir did not show detectable inhibition with the tested conditions. This is the first demonstration of the inhibition of RNA-dependent RNA polymerase activity of NS5 protein from the Kyasanur forest disease virus with small molecule inhibitors. These initial findings can potentially facilitate the discovery and development of targeted therapies for treating Kyasanur forest disease.
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Affiliation(s)
- Mansi Malik
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
| | - Parvathy Vijayan
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
| | - Deepak K Jagannath
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
| | - Rakesh K Mishra
- Tata Institute for Genetics and Society, NCBS campus, GKVK, Bellary Road, Bengaluru, 560065, KA, India
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Cavalleri JV, Korbacska‐Kutasi O, Leblond A, Paillot R, Pusterla N, Steinmann E, Tomlinson J. European College of Equine Internal Medicine consensus statement on equine flaviviridae infections in Europe. Vet Med (Auckl) 2022; 36:1858-1871. [DOI: 10.1111/jvim.16581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022]
Affiliation(s)
- Jessika‐M. V. Cavalleri
- Clinical Unit of Equine Internal Medicine, Department for Companion Animals and Horses University of Veterinary Medicine Vienna Vienna Austria
| | - Orsolya Korbacska‐Kutasi
- Clinical Unit of Equine Internal Medicine, Department for Companion Animals and Horses University of Veterinary Medicine Vienna Vienna Austria
- Department for Animal Breeding, Nutrition and Laboratory Animal Science University of Veterinary Medicine Budapest Hungary
- Hungarian Academy of Sciences—Szent Istvan University (MTA‐SZIE) Large Animal Clinical Research Group Üllő Dóra major Hungary
| | - Agnès Leblond
- EPIA, UMR 0346, Epidemiologie des maladies animales et zoonotiques, INRAE, VetAgro Sup University of Lyon Marcy l'Etoile France
| | - Romain Paillot
- School of Equine and Veterinary Physiotherapy Writtle University College Chelmsford UK
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine University of California Davis California USA
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Faculty of Medicine Ruhr University Bochum Bochum Germany
| | - Joy Tomlinson
- Baker Institute for Animal Health Cornell University College of Veterinary Medicine Ithaca New York USA
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Structural Homology-Based Drug Repurposing Approach for Targeting NSP12 SARS-CoV-2. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227732. [PMID: 36431833 PMCID: PMC9694939 DOI: 10.3390/molecules27227732] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2, also known as SARS-CoV-2, is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 has a highly conserved non-structural protein 12 (NSP-12) involved in RNA-dependent RNA polymerase (RdRp) activity. For the identification of potential inhibitors for NSP-12, computational approaches such as the identification of homologous proteins that have been previously targeted by FDA-approved antivirals can be employed. Herein, homologous proteins of NSP-12 were retrieved from Protein DataBank (PDB) and the evolutionary conserved sequence and structure similarity of the active site of the RdRp domain of NSP-12 was characterized. The identified homologous structures of NSP-12 belonged to four viral families: Coronaviridae, Flaviviridae, Picornaviridae, and Caliciviridae, and shared evolutionary conserved relationships. The multiple sequences and structural alignment of homologous structures showed highly conserved amino acid residues that were located at the active site of the RdRp domain of NSP-12. The conserved active site of the RdRp domain of NSP-12 was evaluated for binding affinity with the FDA-approved antivirals, i.e., Sofosbuvir and Dasabuvir in a molecular docking study. The molecular docking of Sofosbuvir and Dasabuvir with the active site that contains conserved motifs (motif A-G) of the RdRp domain of NSP-12 revealed significant binding affinity. Furthermore, MD simulation also inferred the potency of Sofosbuvir and Dasabuvir. In conclusion, targeting the active site of the RdRp domain of NSP-12 with Dasabuvir and Sofosbuvir might reduce viral replication and pathogenicity and could be further studied for the treatment of SARS-CoV-2.
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Malik AA, Chotpatiwetchkul W, Phanus-Umporn C, Nantasenamat C, Charoenkwan P, Shoombuatong W. StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors. J Comput Aided Mol Des 2021; 35:1037-1053. [PMID: 34622387 DOI: 10.1007/s10822-021-00418-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023]
Abstract
Fast and accurate identification of inhibitors with potency against HCV NS5B polymerase is currently a challenging task. As conventional experimental methods is the gold standard method for the design and development of new HCV inhibitors, they often require costly investment of time and resources. In this study, we develop a novel machine learning-based meta-predictor (termed StackHCV) for accurate and large-scale identification of HCV inhibitors. Unlike the existing method, which is based on single-feature-based approach, we first constructed a pool of various baseline models by employing a wide range of heterogeneous molecular fingerprints with five popular machine learning algorithms (k-nearest neighbor, multi-layer perceptron, partial least squares, random forest and support vectors machine). Secondly, we integrated these baseline models in order to develop the final meta-based model by means of the stacking strategy. Extensive benchmarking experiments showed that StackHCV achieved a more accurate and stable performance as compared to its constituent baseline models on the training dataset and also outperformed the existing predictor on the independent test dataset. To facilitate the high-throughput identification of HCV inhibitors, we built a web server that can be freely accessed at http://camt.pythonanywhere.com/StackHCV . It is expected that StackHCV could be a useful tool for fast and precise identification of potential drugs against HCV NS5B particularly for liver cancer therapy and other clinical applications.
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Affiliation(s)
- Aijaz Ahmad Malik
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Warot Chotpatiwetchkul
- Applied Computational Chemistry Research Unit, Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Chuleeporn Phanus-Umporn
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Phasit Charoenkwan
- Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
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Onawole AT, Sulaiman KO, Kolapo TU, Akinde FO, Adegoke RO. COVID-19: CADD to the rescue. Virus Res 2020; 285:198022. [PMID: 32417181 PMCID: PMC7228740 DOI: 10.1016/j.virusres.2020.198022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]
Abstract
The recent outbreak of the deadly COVID-19 disease, being caused by the novel coronavirus (SARS-CoV-2), has put the world on red alert as it keeps spreading and recording more fatalities. Research efforts are being carried out to curtail the disease from spreading as it has been declared as of global health emergency. Hence, there is an exigent need to identify and design drugs that are capable of curing the infection and hinder its continual spread across the globe. Herein, a computer-aided drug design tool known as the virtual screening method was used to screen a database of 44 million compounds to find compounds that have the potential to inhibit the surface glycoprotein responsible for virus entry and binding. The consensus scoring approach selected three compounds with promising physicochemical properties and favorable molecular interactions with the target protein. These selected compounds can undergo lead optimization to be further developed as drugs that can be used in treating the COVID-19 disease.
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Affiliation(s)
- Abdulmujeeb T Onawole
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261 Saudi Arabia
| | - Kazeem O Sulaiman
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada.
| | - Temitope U Kolapo
- Department of Veterinary Parasitology and Entomology, University of Ilorin,P.M.B. 1515, Ilorin, Nigeria; Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Fatimo O Akinde
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Rukayat O Adegoke
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
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Malik AA, Phanus-Umporn C, Schaduangrat N, Shoombuatong W, Isarankura-Na-Ayudhya C, Nantasenamat C. HCVpred: A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors. J Comput Chem 2020; 41:1820-1834. [PMID: 32449536 DOI: 10.1002/jcc.26223] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/10/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) is one of the major causes of liver disease affecting an estimated 170 million people culminating in 300,000 deaths from cirrhosis or liver cancer. NS5B is one of three potential therapeutic targets against HCV (i.e., the other two being NS3/4A and NS5A) that is central to viral replication. In this study, we developed a classification structure-activity relationship (CSAR) model for identifying substructures giving rise to anti-HCV activities among a set of 578 non-redundant compounds. NS5B inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 independent data splits using the random forest algorithm. The modelability (MODI index) of the data set was determined to be robust with a value of 0.88 exceeding established threshold of 0.65. The predictive performance was deduced by the accuracy, sensitivity, specificity, and Matthews correlation coefficient, which was found to be statistically robust (i.e., the former three parameters afforded values in excess of 0.8 while the latter statistical parameter provided a value >0.7). An in-depth analysis of the top 20 important descriptors revealed that aromatic ring and alkyl side chains are important for NS5B inhibition. Finally, the predictive model is deployed as a publicly accessible HCVpred web server (available at http://codes.bio/hcvpred/) that would allow users to predict the biological activity as being active or inactive against HCV NS5B. Thus, the knowledge and web server presented herein can be used in the design of more potent and specific drugs against the HCV NS5B.
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Affiliation(s)
- Aijaz Ahmad Malik
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chuleeporn Phanus-Umporn
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | | | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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