1
|
Stewart J, Shawon J, Ali MA, Williams B, Shahinuzzaman ADA, Rupa SA, Al-Adhami T, Jia R, Bourque C, Faddis R, Stone K, Sufian MA, Islam R, McShan AC, Rahman KM, Halim MA. Antiviral peptides inhibiting the main protease of SARS-CoV-2 investigated by computational screening and in vitro protease assay. J Pept Sci 2024; 30:e3553. [PMID: 38031661 DOI: 10.1002/psc.3553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in viral replication and transcription and received great attention as a vital target for drug/peptide development. Therapeutic agents such as small-molecule drugs or peptides that interact with the Cys-His present in the catalytic site of Mpro are an efficient way to inhibit the protease. Although several emergency-approved vaccines showed good efficacy and drastically dropped the infection rate, evolving variants are still infecting and killing millions of people globally. While a small-molecule drug (Paxlovid) received emergency approval, small-molecule drugs have low target specificity and higher toxicity. Besides small-molecule drugs, peptide therapeutics are thus gaining increasing popularity as they are easy to synthesize and highly selective and have limited side effects. In this study, we investigated the therapeutic value of 67 peptides targeting Mpro using molecular docking. Subsequently, molecular dynamics (MD) simulations were implemented on eight protein-peptide complexes to obtain molecular-level information on the interaction between these peptides and the Mpro active site, which revealed that temporin L, indolicidin, and lymphocytic choriomeningitis virus (LCMV) GP1 are the best candidates in terms of stability, interaction, and structural compactness. These peptides were synthesized using the solid-phase peptide synthesis protocol, purified by reversed-phase high-performance liquid chromatography (RP-HPLC), and authenticated by mass spectrometry (MS). The in vitro fluorometric Mpro activity assay was used to validate the computational results, where temporin L and indolicidin were observed to be very active against SARS-CoV-2 Mpro with IC50 values of 38.80 and 87.23 μM, respectively. A liquid chromatography-MS (LC-MS) assay was developed, and the IC50 value of temporin L was measured at 23.8 μM. The solution-state nuclear magnetic resonance (NMR) structure of temporin L was determined in the absence of sodium dodecyl sulfate (SDS) micelles and was compared to previous temporin structures. This combined investigation provides critical insights and assists us to further develop peptide inhibitors of SARS-CoV-2 Mpro through structural guided investigation.
Collapse
Affiliation(s)
- James Stewart
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Jakaria Shawon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Blaise Williams
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - A D A Shahinuzzaman
- Pharmaceutical Sciences Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Taha Al-Adhami
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Ruoqing Jia
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cole Bourque
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Ryan Faddis
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Kaylee Stone
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Md Abu Sufian
- School of Pharmacy, Temple University, Philadelphia, PA, USA
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| |
Collapse
|
2
|
Bhattacharya P, Mandal A. Identification of amentoflavone as a potent SARS-CoV-2 M pro inhibitor: a combination of computational studies and in vitro biological evaluation. J Biomol Struct Dyn 2024:1-19. [PMID: 38263736 DOI: 10.1080/07391102.2024.2304676] [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: 08/17/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
Small-molecule inhibitors of SARS-CoV-2 Mpro that block the active site pocket of the viral main protease have been considered potential therapeutics for the development of drugs against SARS-CoV-2. Here, we report the identification of amentoflavone (a biflavonoid) through docking-based virtual screening of a library comprised of 231 compounds consisting of flavonoids and isoflavonoids. The docking results were further substantiated through extensive analysis of the data obtained from all-atom 150 ns MD simulation. End-state effective free energy calculations using MM-PBSA calculations further suggested that (Ra)-amentoflavone (C3'-C8''-atropisomer) may show a greater binding affinity towards the Mpro than (Sa)-amentoflavone. In vitro cytotoxicity assay established that amentoflavone showed a high CC50 value indicating much lower toxicity. Further, potent inhibition of the Mpro by amentoflavone was established by studying the effect on HEK293T cells treated with SARS-CoV-2 Mpro expressing plasmid.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Anirban Mandal
- Department of Microbiology, Mrinalini Datta Mahavidyapith, Kolkata, India
| |
Collapse
|
3
|
Elizalde V, Mirazo S, Romero AH, Alvarez G. In vitro antiviral activity of favipiravir and its 6- and 3-O-substituted derivatives against coronavirus: Acetylation leads to improvement of antiviral activity. Arch Pharm (Weinheim) 2024; 357:e2300494. [PMID: 37853660 DOI: 10.1002/ardp.202300494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
Favipiravir is currently approved for the treatment of the influenza virus and has shown encouraging results in terms of antiviral capacity in clinical studies against severe acute respiratory syndrome coronavirus 2. Favipiravir is a prodrug, where its favipiravir-ribofuranosyl-5B-triphosphate metabolite is capable of blocking RNA replication of the virus. However, the antiviral efficiency of favipiravir is limited by two factors: (i) low accumulation in plasma and rapid excretion/elimination post-administration and (ii) low conversion rate into the active metabolite. To tackle these problems, herein, we have designed new favipiravir analogues focusing on the replacement of the fluorine atom at the 6-position by halogen or hydrogen atoms and 3-O-functionalization with labile groups. The first type of functionalization seeks to increase the antiviral activity because of the better ability of the keto-tautomer as a function of the halogen, and it is hypothesized that the keto-tautomer tends to promote the formation of the ribofuranosyl-5B-triphosphate (RTP) metabolite. Meanwhile, the second type of functionalization seeks to promote lipophilicity and increase accumulation in cells. From the in vitro antiviral activity against two coronavirus models (bovine and human 229E), it was identified that the replacement did not improve the antiviral activity against both the models, which seems to be attributable to the low water solubility of these new 6-functionalized analogues. Meanwhile, with 3-O-functionalization, acetylation provided the most active compounds with higher half-maximal inhibitory concentration and selectivity than favipiravir, whereas benzylation/methanosulfonation yielded the least active compounds. In summary, acetylation is found to be a convenient functionalization to enhance the antiviral profile of favipiravir.
Collapse
Affiliation(s)
- Valeria Elizalde
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Santiago Mirazo
- Depertamento de Bacteriología y Virología. Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Angel H Romero
- Grupo de Química Orgánica Medicinal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Guzman Alvarez
- Laboratorio de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú, Uruguay
| |
Collapse
|
4
|
Jash R, Prasanth DSNBK, Jash M, Suneetha A. Small molecules in the race of COVID-19 drug development. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2023; 25:1133-1154. [PMID: 37066495 DOI: 10.1080/10286020.2023.2197595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
COVID-19, caused by SARS-CoV-2, is spreading worldwide, regardless of different continents, increasing the death toll to almost five million, with more than 300 million reported cases. Researchers have been fighting the greatest threats to human civilization. This report provides a glimpse of ongoing small-molecule research on COVID-19 drugs to save millions of lives, which may provide researchers with a better understanding of rigorously investigated therapeutic agents. This report emphasizes the chemical structures and mechanisms of activity along with drug target information for several small molecules, including marketable drugs and agents under investigation.
Collapse
Affiliation(s)
- Rajiv Jash
- Department of Pharmacy, Sanaka Educational Trust Group of Institutions, Durgapur, West Bengal 713 212, India
| | - D S N B K Prasanth
- Department of Pharmacognosy, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh 520 010, India
| | - Moumita Jash
- Department of Pharmacy, Sanaka Educational Trust Group of Institutions, Durgapur, West Bengal 713 212, India
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan 342037, India
| | - Achanti Suneetha
- Department of Pharmaceutical Analysis, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh 520 010, India
| |
Collapse
|
5
|
Romero AH, Fuentes G, Suescun L, Piro O, Echeverría G, Gotopo L, Pezaroglo H, Álvarez G, Cabrera G, Cerecetto H, Couto M. Tautomerism and Rotamerism of Favipiravir and Halogenated Analogues in Solution and in the Solid State. J Org Chem 2023; 88:10735-10752. [PMID: 37452781 DOI: 10.1021/acs.joc.3c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Favipiravir is an important selective antiviral against RNA-based viruses, and currently, it is being repurposed as a potential drug for the treatment of COVID-19. This type of chemical system presents different carboxamide-rotameric and hydroxyl-tautomeric states, which could be essential for interpreting its selective antiviral activity. Herein, the tautomeric 3-hydroxypyrazine/3-pyrazinone pair of favipiravir and its 6-substituted analogues, 6-Cl, 6-Br, 6-I, and 6-H, were fully investigated in solution and in the solid state through ultraviolet-visible, 1H nuclear magnetic resonance, infrared spectroscopy, and X-ray diffraction techniques. Also, a study of the gas phase was performed using density functional theory calculations. In general, the keto-enol balance in these 3-hydroxy-2-pyrazinecarboxamides is finely modulated by external and internal electrical variations via changes in solvent polarity or by replacement of substituents at position 6. The enol tautomer was prevalent in an apolar environment, whereas an increase in the level of the keto tautomer was favored by an increase in solvent polarity and, even moreso, with a strong hydrogen-donor solvent. Keto tautomerization was favored either in solution or in the solid state with a decrease in 6-substituent electronegativity as follows: H ≫ I ≈ Br > Cl ≥ F. Specific rotameric states based on carboxamide, "cisoide" and "transoide", were identified for the enol and keto tautomer, respectively; their rotamerism is dependent on the tautomerism and not the aggregation state.
Collapse
Affiliation(s)
- Angel H Romero
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Germán Fuentes
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Leopoldo Suescun
- Cryssmat-Lab/DETEMA, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Oscar Piro
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, La Plata 1900, Argentina
| | - Gustavo Echeverría
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, La Plata 1900, Argentina
| | - Lourdes Gotopo
- Laboratorio de Síntesis Orgánica, Escuela de Química, Facultad de Ciencias, Universidad Central de Venezuela, Los Chaguaramos, 1040 Caracas, Venezuela
| | - Horacio Pezaroglo
- Laboratorio de Resonancia Magnética Nuclear, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Guzmán Álvarez
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Gustavo Cabrera
- Laboratorio de Síntesis Orgánica, Escuela de Química, Facultad de Ciencias, Universidad Central de Venezuela, Los Chaguaramos, 1040 Caracas, Venezuela
| | - Hugo Cerecetto
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
- Area de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
| | - Marcos Couto
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| |
Collapse
|
6
|
Cardoza S, Shrivash MK, Riva L, Chatterjee AK, Mandal A, Tandon V. Multistep Synthesis of Analogues of Remdesivir: Incorporating Heterocycles at the C-1' Position. J Org Chem 2023; 88:9105-9122. [PMID: 37276453 DOI: 10.1021/acs.joc.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Studies suggest that the 1'β-CN moiety in remdesivir sterically clashes with the Ser861 residue of the RNA-dependent-RNA polymerase (RdRp), causing a delayed chain termination in the RNA replication process. Replacing C1'β-CN with 5-membered heterocycles such as tetrazoles, oxadiazoles, and triazoles can augment the inhibitory activity and pharmacokinetic profile of C-nucleotides. Synthesis of tetrazole-, triazole-, and oxadiazole-integrated C1' analogues of remdesivir was attempted using general synthetic routes. The final compounds 26, 28, and 29 did not inhibit viral replication; however, the synthetic intermediates, i.e., 27 and 50, exhibited an IC90 = 14.1 μM each. The trifluoromethyl-substituted 1,2,4-oxadiazole 59 showed an IC90 of 33.5 μM. This work adds to the growing evidence of the beneficial medicinal impact of C1,1'-disubstituted C-nucleotides.
Collapse
Affiliation(s)
- Savio Cardoza
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Kumar Shrivash
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211012, Uttar Pradesh, India
| | - Laura Riva
- Calibr, Scripps Research, La Jolla, 11119 North Torrey Pines Road Suite 100, California 92037, United States
| | - Arnab K Chatterjee
- Calibr, Scripps Research, La Jolla, 11119 North Torrey Pines Road Suite 100, California 92037, United States
| | - Ajay Mandal
- Symbol Discovery Ltd, ASPIRE-TBI, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
7
|
Castillo-Campos L, Velázquez-Libera JL, Caballero J. Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2023; 10:1215499. [PMID: 37426421 PMCID: PMC10326900 DOI: 10.3389/fmolb.2023.1215499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
Collapse
|
8
|
Vaz ES, Vassiliades SV, Giarolla J, Polli MC, Parise-Filho R. Drug repositioning in the COVID-19 pandemic: fundamentals, synthetic routes, and overview of clinical studies. Eur J Clin Pharmacol 2023; 79:723-751. [PMID: 37081137 PMCID: PMC10118228 DOI: 10.1007/s00228-023-03486-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023]
Abstract
INTRODUCTION Drug repositioning is a strategy to identify a new therapeutic indication for molecules that have been approved for other conditions, aiming to speed up the traditional drug development process and reduce its costs. The high prevalence and incidence of coronavirus disease 2019 (COVID-19) underline the importance of searching for a safe and effective treatment for the disease, and drug repositioning is the most rational strategy to achieve this goal in a short period of time. Another advantage of repositioning is the fact that these compounds already have established synthetic routes, which facilitates their production at the industrial level. However, the hope for treatment cannot allow the indiscriminate use of medicines without a scientific basis. RESULTS The main small molecules in clinical trials being studied to be potentially repositioned to treat COVID-19 are chloroquine, hydroxychloroquine, ivermectin, favipiravir, colchicine, remdesivir, dexamethasone, nitazoxanide, azithromycin, camostat, methylprednisolone, and baricitinib. In the context of clinical tests, in general, they were carried out under the supervision of large consortiums with a methodology based on and recognized in the scientific community, factors that ensure the reliability of the data collected. From the synthetic perspective, compounds with less structural complexity have more simplified synthetic routes. Stereochemical complexity still represents the major challenge in the preparation of dexamethasone, ivermectin, and azithromycin, for instance. CONCLUSION Remdesivir and baricitinib were approved for the treatment of hospitalized patients with severe COVID-19. Dexamethasone and methylprednisolone should be used with caution. Hydroxychloroquine, chloroquine, ivermectin, and azithromycin are ineffective for the treatment of the disease, and the other compounds presented uncertain results. Preclinical and clinical studies should not be analyzed alone, and their methodology's accuracy should also be considered. Regulatory agencies are responsible for analyzing the efficacy and safety of a treatment and must be respected as the competent authorities for this decision, avoiding the indiscriminate use of medicines.
Collapse
Affiliation(s)
- Elisa Souza Vaz
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil
| | - Sandra Valeria Vassiliades
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil
| | - Michelle Carneiro Polli
- Pharmacy Course, São Francisco University (USF), Waldemar César da Silveira St, 105, SP, Campinas, Brazil
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Prof. Lineu Prestes Avenue, 580, Bldg 13, SP, São Paulo, Brazil.
| |
Collapse
|
9
|
Raghav PK, Mann Z, Ahluwalia SK, Rajalingam R. Potential treatments of COVID-19: Drug repurposing and therapeutic interventions. J Pharmacol Sci 2023; 152:1-21. [PMID: 37059487 PMCID: PMC9930377 DOI: 10.1016/j.jphs.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The infection is caused when Spike-protein (S-protein) present on the surface of SARS-CoV-2 interacts with human cell surface receptor, Angiotensin-converting enzyme 2 (ACE2). This binding facilitates SARS-CoV-2 genome entry into the human cells, which in turn causes infection. Since the beginning of the pandemic, many different therapies have been developed to combat COVID-19, including treatment and prevention. This review is focused on the currently adapted and certain other potential therapies for COVID-19 treatment, which include drug repurposing, vaccines and drug-free therapies. The efficacy of various treatment options is constantly being tested through clinical trials and in vivo studies before they are made medically available to the public.
Collapse
Affiliation(s)
- Pawan Kumar Raghav
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
| | | | - Simran Kaur Ahluwalia
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh, India
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
10
|
Hosseini-Gerami L, Higgins IA, Collier DA, Laing E, Evans D, Broughton H, Bender A. Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis. BMC Bioinformatics 2023; 24:154. [PMID: 37072707 PMCID: PMC10111792 DOI: 10.1186/s12859-023-05277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/06/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Elucidating compound mechanism of action (MoA) is beneficial to drug discovery, but in practice often represents a significant challenge. Causal Reasoning approaches aim to address this situation by inferring dysregulated signalling proteins using transcriptomics data and biological networks; however, a comprehensive benchmarking of such approaches has not yet been reported. Here we benchmarked four causal reasoning algorithms (SigNet, CausalR, CausalR ScanR and CARNIVAL) with four networks (the smaller Omnipath network vs. 3 larger MetaBase™ networks), using LINCS L1000 and CMap microarray data, and assessed to what extent each factor dictated the successful recovery of direct targets and compound-associated signalling pathways in a benchmark dataset comprising 269 compounds. We additionally examined impact on performance in terms of the functions and roles of protein targets and their connectivity bias in the prior knowledge networks. RESULTS According to statistical analysis (negative binomial model), the combination of algorithm and network most significantly dictated the performance of causal reasoning algorithms, with the SigNet recovering the greatest number of direct targets. With respect to the recovery of signalling pathways, CARNIVAL with the Omnipath network was able to recover the most informative pathways containing compound targets, based on the Reactome pathway hierarchy. Additionally, CARNIVAL, SigNet and CausalR ScanR all outperformed baseline gene expression pathway enrichment results. We found no significant difference in performance between L1000 data or microarray data, even when limited to just 978 'landmark' genes. Notably, all causal reasoning algorithms also outperformed pathway recovery based on input DEGs, despite these often being used for pathway enrichment. Causal reasoning methods performance was somewhat correlated with connectivity and biological role of the targets. CONCLUSIONS Overall, we conclude that causal reasoning performs well at recovering signalling proteins related to compound MoA upstream from gene expression changes by leveraging prior knowledge networks, and that the choice of network and algorithm has a profound impact on the performance of causal reasoning algorithms. Based on the analyses presented here this is true for both microarray-based gene expression data as well as those based on the L1000 platform.
Collapse
Affiliation(s)
- Layla Hosseini-Gerami
- Department of Chemistry, Centre for Molecular Informatics, Cambridge, UK
- Ignota Labs, London, UK
| | | | - David A Collier
- Eli Lilly and Company, Bracknell, UK
- Social, Genetic and Developmental Psychiatry Centre, IoPPN, Kings's College London, London, UK
- Genetic and Genomic Consulting Ltd, Farnham, UK
| | - Emma Laing
- Eli Lilly and Company, Bracknell, UK
- GSK, Stevenage, UK
| | - David Evans
- Eli Lilly and Company, Bracknell, UK
- DeepMind, London, UK
| | - Howard Broughton
- Centre de Investigación, Eli Lilly and Company, Alcobendas, Spain
| | - Andreas Bender
- Department of Chemistry, Centre for Molecular Informatics, Cambridge, UK.
| |
Collapse
|
11
|
Potential Anti-SARS-CoV-2 Prodrugs Activated by Phosphorylation and Their Role in the Aged Population. Molecules 2023; 28:molecules28052332. [PMID: 36903575 PMCID: PMC10004871 DOI: 10.3390/molecules28052332] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The COVID-19 pandemic has flared across every part of the globe and affected populations from different age groups differently. People aged from 40 to 80 years or older are at an increased risk of morbidity and mortality due to COVID-19. Therefore, there is an urgent requirement to develop therapeutics to decrease the risk of the disease in the aged population. Over the last few years, several prodrugs have demonstrated significant anti-SARS-CoV-2 effects in in vitro assays, animal models, and medical practice. Prodrugs are used to enhance drug delivery by improving pharmacokinetic parameters, decreasing toxicity, and attaining site specificity. This article discusses recently explored prodrugs such as remdesivir, molnupiravir, favipiravir, and 2-deoxy-D-glucose (2-DG) and their implications in the aged population, as well as investigating recent clinical trials.
Collapse
|
12
|
Banik S, Adarsh D, Reddy BS. Three-step process for the synthesis of favipiravir. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023] Open
|
13
|
Blaskovich MAT, Verderosa AD. Use of Antiviral Agents and other Therapies for COVID-19. Semin Respir Crit Care Med 2023; 44:118-129. [PMID: 36646090 DOI: 10.1055/s-0042-1758837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic led to a remarkably rapid development of a range of effective prophylactic vaccines, including new technologies that had not previously been approved for human use. In contrast, the development of new small molecule antiviral therapeutics has taken years to produce the first approved drugs specifically targeting severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), with the intervening years filled with attempts to repurpose existing drugs and the development of biological therapeutics. This review will discuss the reasons behind this variation in timescale and provide a survey of the many new treatments that are progressing through the clinical pipeline.
Collapse
Affiliation(s)
- Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Anthony D Verderosa
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| |
Collapse
|
14
|
Singh R, Kumar Tyagi Y, Yadav N. Hydroxychloroquine: Chemistry and Medicinal Applications. HETEROCYCLES 2023. [DOI: 10.3987/rev-22-993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
15
|
Jayabal K, Elumalai D, Leelakrishnan S, Bhattacharya S, Rengarajan V, Kannan T, Chuang SC. Green and Regioselective Approach for the Synthesis of 3-Substituted Indole Based 1,2-Dihydropyridine and Azaxanthone Derivatives as a Potential Lead for SARS-CoV-2 and Delta Plus Mutant Virus: DFT and Docking Studies. ACS OMEGA 2022; 7:43856-43876. [PMID: 36506171 PMCID: PMC9730777 DOI: 10.1021/acsomega.2c04990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Great attempts have been done for the development of novel antiviral compounds against SAR-CoV-2 to end this pandemic situation and save human society. Herewith, we have synthesized 3-substituted indole/2-substituted pyrrole 1,2-dihydropyridine and azaxanthone scaffolds using simple, commercially available starting materials in a one-pot, green, and regioselective manner. Further, the regioselectivity of product formation was confirmed by various studies such as controlled experiments, density functional theory (DFT), Mulliken atomic charge, and electrostatic potential (ESP) surface. In addition, 3-substituted indole 1,2-dihydropyridine was successfully converted into a biologically enriched pharmacophore scaffold, viz., indolylimidazopyridinylbenzofuran scaffold, in excellent yield. Moreover, the synthesized 3-substituted indole 1,2-dihydropyridine/2-substituted pyrroles were analyzed in docking studies for anti-SARS-CoV-2 properties against their main protease (Mpro) and anti-Delta plus properties against their protein of the Delta plus K417N mutant. Further, the drug-likeness prediction was analyzed by the Lipinski rule and other pharmacokinetic properties like absorption, distribution, metabolism, excretion, and toxicity using preADMET prediction. Interestingly, the docking results show that out of 20 synthesized compounds, 5 of them for Mpro of SAR-CoV-2 and 9 of them for 7NX7 spike glycoprotein's A chain of Delta plus K417N show greater binding affinity when compared with remdesivir that is the first to receive FDA approval and is currently used as a potent drug for the treatment of COVID-19. These results suggest that indole/pyrrole substituted 1,2-dihydropyridine derivatives are capable of combating SARS-CoV-2 and its Delta plus mutant.
Collapse
Affiliation(s)
- Kamalraja Jayabal
- Department
of Chemistry, Pondicherry University, Puducherry 605014, India
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, Hsinchu 30010, Taiwan R.O.C
| | | | - Saraswathi Leelakrishnan
- Department
of Chemistry, Pondicherry University, Puducherry 605014, India
- Department
of Chemistry, Nirmala College for Women, Coimbatore 641018, India
| | - Suman Bhattacharya
- Department
of Physics, University of Limerick, Castletroy, Limerick V94
T9PX , Republic of Ireland
| | | | | | - Shih-Ching Chuang
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, Hsinchu 30010, Taiwan R.O.C
| |
Collapse
|
16
|
Pathfinder-Driven Chemical Space Exploration and Multiparameter Optimization in Tandem with Glide/IFD and QSAR-Based Active Learning Approach to Prioritize Design Ideas for FEP+ Calculations of SARS-CoV-2 PL pro Inhibitors. Molecules 2022; 27:molecules27238569. [PMID: 36500659 PMCID: PMC9741453 DOI: 10.3390/molecules27238569] [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: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
A global pandemic caused by the SARS-CoV-2 virus that started in 2020 and has wreaked havoc on humanity still ravages up until now. As a result, the negative impact of travel restrictions and lockdowns has underscored the importance of our preparedness for future pandemics. The main thrust of this work was based on addressing this need by traversing chemical space to design inhibitors that target the SARS-CoV-2 papain-like protease (PLpro). Pathfinder-based retrosynthesis analysis was used to generate analogs of GRL-0617 using commercially available building blocks by replacing the naphthalene moiety. A total of 10 models were built using active learning QSAR, which achieved good statistical results such as an R2 > 0.70, Q2 > 0.64, STD Dev < 0.30, and RMSE < 0.31, on average for all models. A total of 35 ideas were further prioritized for FEP+ calculations. The FEP+ results revealed that compound 45 was the most active compound in this series with a ΔG of −7.28 ± 0.96 kcal/mol. Compound 5 exhibited a ΔG of −6.78 ± 1.30 kcal/mol. The inactive compounds in this series were compound 91 and compound 23 with a ΔG of −5.74 ± 1.06 and −3.11 ± 1.45 kcal/mol. The combined strategy employed here is envisaged to be of great utility in multiparameter lead optimization efforts, to traverse chemical space, maintaining and/or improving the potency as well as the property space of synthetically aware design ideas.
Collapse
|
17
|
Salarizadeh N, Aallaei MR, Zarei A, Malekshah RE, Molaakbari E, Farajnezhadi A. Docking and Molecular Dynamics Simulations of Flavonoids as Inhibitors of Infectious Agents: Rutin as a Coronavirus Protease Inhibitor. ChemistrySelect 2022. [DOI: 10.1002/slct.202202043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Navvabeh Salarizadeh
- Department of Cell & Molecular Biology School of Biology College of Science University of Tehran Tehran Iran
- School of Medicine Baqyatallah University of Medical Sciences Tehran Iran
| | | | - Ali Zarei
- School of Medicine Baqyatallah University of Medical Sciences Tehran Iran
| | | | - Elaheh Molaakbari
- Department of Chemistry Shahid Bahonar University of Kerman Kerman Iran
| | - Amirreza Farajnezhadi
- School of Chemical Engineering College of Engineering University of Tehran Tehran Iran
| |
Collapse
|
18
|
Askari FS, Ebrahimi M, Parhiz J, Hassanpour M, Mohebbi A, Mirshafiey A. Digging for the discovery of SARS-CoV-2 nsp12 inhibitors: a pharmacophore-based and molecular dynamics simulation study. Future Virol 2022. [PMID: 35983350 PMCID: PMC9370102 DOI: 10.2217/fvl-2022-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022]
Abstract
Aim: COVID-19 is a global health threat. Therapeutics are urgently needed to cure patients severely infected with COVID-19. Objective: to investigate potential candidates of nsp12 inhibitors by searching for druggable cavity pockets within the viral protein and drug discovery. Methods: A virtual screening of ZINC natural products on SARS-CoV-2 nsp12's druggable cavity was performed. A lead compound with the highest affinity to nsp12 was simulated dynamically for 10 ns. Results: ZINC03977803 was nominated as the lead compound. The results showed stable interaction between ZINC03977803 and nsp12 during 10 ns. Discussion: ZINC03977803 showed stable interaction with the catalytic subunit of SARS-CoV-2, nsp12. It could inhibit the SARS-CoV-2 life cycle by direct interaction with nsp12 and inhibit RdRp complex formation.
Collapse
Affiliation(s)
| | - Mohsen Ebrahimi
- Neonatal & Children's Health Research Center, Golestan University of Medical Sciences, Gorgan, 4918936316, Iran
| | - Jabbar Parhiz
- Neonatal & Children's Health Research Center, Golestan University of Medical Sciences, Gorgan, 4918936316, Iran
| | - Mina Hassanpour
- Vista Aria Rena Gene Inc., Gorgan, 4918653885, Golestan Province, Iran
| | - Alireza Mohebbi
- Vista Aria Rena Gene Inc., Gorgan, 4918653885, Golestan Province, Iran
| | - Abbas Mirshafiey
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, 1417613151, Iran
| |
Collapse
|
19
|
Concise synthesis of antiviral drug, Molnupiravir by direct coupling of fully protected D-Ribose with cytosine. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
20
|
Stevens AC, Brak K, Bremner WS, Brown AM, Chtchemelinine A, Heumann L, Kerschen JA, Subotkowski W, Vieira T, Wolfe LC, Xu B, Yu CY. Development of a Scalable Lanthanide Halide/Quaternary Ammonium Salt System for the Nucleophilic Addition of Grignard Reagents to Carbonyl Groups and Application to the Synthesis of a Remdesivir Intermediate. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew C. Stevens
- Gilead Alberta ULC, 1021 Hayter Road, Edmonton, Alberta T6S 1A1, Canada
| | - Katrien Brak
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - W. Stacy Bremner
- Gilead Alberta ULC, 1021 Hayter Road, Edmonton, Alberta T6S 1A1, Canada
| | - Angela M. Brown
- J-Star Research Inc., 3001 Hadley Road #3, South Plainsfield, New Jersey 07080, United States
| | - Andrei Chtchemelinine
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Lars Heumann
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - James A. Kerschen
- J-Star Research Inc., 3001 Hadley Road #3, South Plainsfield, New Jersey 07080, United States
| | - Witold Subotkowski
- J-Star Research Inc., 3001 Hadley Road #3, South Plainsfield, New Jersey 07080, United States
| | - Tiago Vieira
- Gilead Alberta ULC, 1021 Hayter Road, Edmonton, Alberta T6S 1A1, Canada
| | - Lydia C. Wolfe
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| | - Boran Xu
- Gilead Alberta ULC, 1021 Hayter Road, Edmonton, Alberta T6S 1A1, Canada
| | - Chia-Yun Yu
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States
| |
Collapse
|
21
|
Mahato S. Recent Development of Small Molecules for SARS-CoV-2 and the Opportunity for Fragment-Based Drug Discovery. Med Chem 2022; 18:847-858. [DOI: 10.2174/1573406418666220214091107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/10/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
The ongoing pandemic of Covid-19 caused by SARS-CoV-2 is a major threat to global public health, drawing attention to develop new therapeutics for treatment. Much research work is focused on identifying or repurposing new small molecules to serve as potential inhibitors by interacting with viral or host-cell molecular targets and understanding the nature of the virus in the host cells. Identifying small molecules as potent inhibitors at an early stage is advantageous to make a molecule with higher potency and then find a lead compound for the development of drug discovery. Small molecules can show their inhibition property by targeting either SARS-CoV-2 main protease (Mpro) enzyme, papain-like protease (PLpro) enzyme, or helicase (Hel), or blocking the spike (S) protein angiotensin-converting enzyme 2 (ACE2) receptor. A very recent outbreak of a new variant (B.1.617.2—termed as Delta variant) of SARS-CoV-2 worldwide posed a greater challenge as it is resistant to clinically undergoing vaccine trials. Thus, the development of new drug molecules is of potential interest to combat SARS-CoV-2 disease, and for that, fragment-based drug discovery (FBDD) approach could be one of the ways to bring out an effective solution. Two cysteine protease enzymes would be an attractive choice of target for fragment-based drug discovery to tune the molecular structure at an early stage with suitable functionality. In this short review, the recent development of small-molecule as inhibitors against Covid-19 are discussed and the opportunity for FBDD is envisioned optimistically to provide an outlook regarding Covid-19 that may pave the way in the direction of the Covid-19 drug development paradigm.
Collapse
Affiliation(s)
- Sujit Mahato
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, Gujarat-395007, INDIA
| |
Collapse
|
22
|
Obradors C, Mitschke B, Aukland MH, Leutzsch M, Grossmann O, Brunen S, Schwengers SA, List B. Direkte Katalytische
C
‐Glykosylierung von Arenen: beschleunigte Synthese des Remdesivir‐Nucleosids**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Carla Obradors
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Benjamin Mitschke
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Miles H. Aukland
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Markus Leutzsch
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Oleg Grossmann
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Sebastian Brunen
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Sebastian A. Schwengers
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Benjamin List
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| |
Collapse
|
23
|
Roy S, Yadaw A, Roy S, Sirasani G, Gangu A, Brown JD, Armstrong JD, Stringham RW, Gupton BF, Senanayake CH, Snead DR. Facile and Scalable Methodology for the Pyrrolo[2,1- f][1,2,4]triazine of Remdesivir. Org Process Res Dev 2022; 26:82-90. [PMID: 35095258 PMCID: PMC8787819 DOI: 10.1021/acs.oprd.1c00071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 12/26/2022]
Abstract
Pyrrolo[2,1-f][1,2,4]triazine (1) is an important regulatory starting material in the production of the antiviral drug remdesivir. Compound 1 was produced through a newly developed synthetic methodology utilizing simple building blocks such as pyrrole, chloramine, and formamidine acetate by examining the mechanistic pathway for the process optimization exercise. Triazine 1 was obtained in 55% overall yield in a two-vessel-operated process. This work describes the safety of the process, impurity profiles and control, and efforts toward the scale-up of triazine for the preparation of kilogram quantity.
Collapse
Affiliation(s)
- Sarabindu Roy
- Kolkata
- R&D Centre, TCG Lifesciences Private
Limited, Chemistry, Block
BN, Plot 7, Salt Lake Electronics Complex, Sector V, Kolkata, West Bengal 700091, India
| | - Ajay Yadaw
- Kolkata
- R&D Centre, TCG Lifesciences Private
Limited, Chemistry, Block
BN, Plot 7, Salt Lake Electronics Complex, Sector V, Kolkata, West Bengal 700091, India
| | - Subho Roy
- Kolkata
- R&D Centre, TCG Lifesciences Private
Limited, Chemistry, Block
BN, Plot 7, Salt Lake Electronics Complex, Sector V, Kolkata, West Bengal 700091, India
| | - Gopal Sirasani
- TCG
GreenChem, Inc., 737
North 5th Street, Suite 467, Richmond, Virginia 23219, United States
| | - Aravind Gangu
- TCG
GreenChem, Inc., 737
North 5th Street, Suite 467, Richmond, Virginia 23219, United States
| | - Jack D. Brown
- TCG
GreenChem, Inc., 737
North 5th Street, Suite 467, Richmond, Virginia 23219, United States
| | - Joseph D. Armstrong
- TCG
GreenChem, Inc., 737
North 5th Street, Suite 467, Richmond, Virginia 23219, United States
| | - Rodger W. Stringham
- Medicines
for All Institute, 737
N 5th Street, Box 980100, Richmond, Virginia 23298, United
States
| | - B. Frank Gupton
- Medicines
for All Institute, 737
N 5th Street, Box 980100, Richmond, Virginia 23298, United
States
| | - Chris H. Senanayake
- TCG
GreenChem, Inc., 737
North 5th Street, Suite 467, Richmond, Virginia 23219, United States
| | - David R. Snead
- Medicines
for All Institute, 737
N 5th Street, Box 980100, Richmond, Virginia 23298, United
States
| |
Collapse
|
24
|
Acharya Y, Bhattacharyya S, Dhanda G, Haldar J. Emerging Roles of Glycopeptide Antibiotics: Moving beyond Gram-Positive Bacteria. ACS Infect Dis 2022; 8:1-28. [PMID: 34878254 DOI: 10.1021/acsinfecdis.1c00367] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glycopeptides, a class of cell wall biosynthesis inhibitors, have been the antibiotics of choice against drug-resistant Gram-positive bacterial infections. Their unique mechanism of action involving binding to the substrate of cell wall biosynthesis and substantial longevity in clinics makes this class of antibiotics an attractive choice for drug repurposing and reprofiling. However, resistance to glycopeptides has been observed due to alterations in the substrate, cell wall thickening, or both. The emergence of glycopeptide resistance has resulted in the development of synthetic and semisynthetic glycopeptide analogues to target acquired resistance. Recent findings demonstrate that these derivatives, along with some of the FDA approved glycopeptides have been shown to have antimicrobial activity against Gram-negative bacteria, Mycobacteria, and viruses thus expanding their spectrum of activity across the microbial kingdom. Additional mechanisms of action and identification of novel targets have proven to be critical in broadening the spectrum of activity of glycopeptides. This review focuses on the applications of glycopeptides beyond their traditional target group of Gram-positive bacteria. This will aid in making the scientific community aware about the nontraditional activity profiles of glycopeptides, identify the existing loopholes, and further explore this antibiotic class as a potential broad-spectrum antimicrobial agent.
Collapse
Affiliation(s)
- Yash Acharya
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Shaown Bhattacharyya
- Biochemistry and Molecular Biology Program, Departments of Chemistry and Biology, College of Arts and Science, Boston University, Boston, Massachusetts 02215, United States
| | - Geetika Dhanda
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
- School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| |
Collapse
|
25
|
Kumar Palli K, Ghosh P, Krishna Avula S, Sridhara Shanmukha Rao B, Patil AD, Ghosh S, Sudhakar G, Raji Reddy C, Mainkar PS, Chandrasekhar S. Total synthesis of remdesivir. Tetrahedron Lett 2022; 88:153590. [PMID: 34908617 PMCID: PMC8656175 DOI: 10.1016/j.tetlet.2021.153590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Remdesivir, the first drug approved by the FDA to treat COVID-19, is in high demand for patients infected with the SARS-CoV-2 virus. Herein, we report a facile approach minimizing the protecting group manipulations to afford remdesivir in good overall yield.
Collapse
Affiliation(s)
- Kishore Kumar Palli
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Palash Ghosh
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shiva Krishna Avula
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - B. Sridhara Shanmukha Rao
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amol D. Patil
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Subhash Ghosh
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gangarajula Sudhakar
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Chada Raji Reddy
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prathama S. Mainkar
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Srivari Chandrasekhar
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India,Corresponding author at: Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| |
Collapse
|
26
|
KÜÇÜK BEYZANUR, ŞİMŞEK RAHİME, ERDEMLİ KÖSE SELİNAYBAŞAK, YİRÜN ANIL, Erkekoglu P. Adverse Effects of COVID-19 Treatments: A Special Focus on Susceptible Populations. J Environ Pathol Toxicol Oncol 2022; 41:45-64. [DOI: 10.1615/jenvironpatholtoxicoloncol.2022039271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
27
|
List B, Obradors C, Mitschke B, Aukland M, Leutzsch M, Grossmann O, Brunen S, Schwengers S. Direct and Catalytic C-Glycosylation of Arenes: Expeditious Synthesis of the Remdesivir Nucleoside. Angew Chem Int Ed Engl 2021; 61:e202114619. [PMID: 34856043 PMCID: PMC9305923 DOI: 10.1002/anie.202114619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Indexed: 12/01/2022]
Abstract
Since early 2020, scientists have strived to find an effective solution to fight SARS‐CoV‐2, in particular by developing reliable vaccines that inhibit the spread of the disease and repurposing drugs for combatting its effects on the human body. The antiviral prodrug Remdesivir is still the most widely used therapeutic during the early stages of the infection. However, the current synthetic routes rely on the use of protecting groups, air‐sensitive reagents, and cryogenic conditions, thus impeding a cost‐efficient supply to patients. We have, therefore, focused on the development of a straightforward, direct addition of (hetero)arenes to unprotected sugars. Here we report a silylium‐catalyzed and completely stereoselective C‐glycosylation that initially yields the open‐chain polyols, which can be selectively cyclized to provide either the kinetic α‐furanose or the thermodynamically favored β‐anomer. The method significantly expedites the synthesis of Remdesivir precursor GS‐441524 after a subsequent Mn‐catalyzed C−H oxidation and deoxycyanation.
Collapse
Affiliation(s)
- Benjamin List
- Max-Planck-Institut für Kohlenforschung, Homogenous Catalysis, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, GERMANY
| | - Carla Obradors
- Max-Planck-Institut für Kohlenforschung, Homogeneous Catalysis, GERMANY
| | - Benjamin Mitschke
- Max-Planck-Institut für Kohlenforschung, Homogeneous Catalysis, GERMANY
| | - Miles Aukland
- Max-Planck-Institut für Kohlenforschung, Homogeneous Catalysis, GERMANY
| | - Markus Leutzsch
- Max Planck Institute of Coal Research: Max-Planck-Institut fur Kohlenforschung, Homogeneous Catalysis, GERMANY
| | - Oleg Grossmann
- Max Planck Institute of Coal Research: Max-Planck-Institut fur Kohlenforschung, Homogeneous Catalysis, GERMANY
| | - Sebastian Brunen
- Max Planck Institute of Coal Research: Max-Planck-Institut fur Kohlenforschung, Homogeneous Catalysis, GERMANY
| | - Sebastian Schwengers
- Max Planck Institute of Coal Research: Max-Planck-Institut fur Kohlenforschung, Homogeneous Catalysis, GERMANY
| |
Collapse
|
28
|
Bioeconomy during the COVID-19 and perspectives for the post-pandemic world: Example from EU. EFB BIOECONOMY JOURNAL 2021. [PMCID: PMC8683579 DOI: 10.1016/j.bioeco.2021.100013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
29
|
Qin Z, Dong B, Wang R, Huang D, Wang J, Feng X, Bian J, Li Z. Preparing anti-SARS-CoV-2 agent EIDD-2801 by a practical and scalable approach, and quick evaluation via machine learning. Acta Pharm Sin B 2021; 11:3678-3682. [PMID: 34703727 PMCID: PMC8529884 DOI: 10.1016/j.apsb.2021.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
EIDD-2801 is an orally bioavailable prodrug, which will be applied for emergency use authorization from the U.S. Food and Drug Administration for the treatment of COVID-19. To investigate the optimal parameters, EIDD-2801 was optimized via a four-step synthesis with high purity of 99.9%. The hydroxylamination procedure was telescoped in a one-pot and the final step was precisely controlled on reagents, temperature and reaction time. Compared to the original route, the yield of the new route was enhanced from 17% to 58% without column chromatography. The optimized synthesis has been successfully determinated on a decagram scale: the first step at 200 g and the final step at 20 g. Besides, the relationship between yield and temperature, time, and reagents in the deprotection step was investigated via Shapley value explanation and machine learning approach-decision tree method. The results revealed that reagents have the greatest impact on yield estimation, followed by the temperature.
Collapse
Affiliation(s)
- Zhen Qin
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, China
| | - Bin Dong
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211100, China
| | - Renbing Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, China
| | - Dechun Huang
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211100, China
| | - Jubo Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, China
| | - Xi Feng
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, China
| |
Collapse
|
30
|
Jain S, Talley DC, Baljinnyam B, Choe J, Hanson Q, Zhu W, Xu M, Chen CZ, Zheng W, Hu X, Shen M, Rai G, Hall MD, Simeonov A, Zakharov AV. Hybrid In Silico Approach Reveals Novel Inhibitors of Multiple SARS-CoV-2 Variants. ACS Pharmacol Transl Sci 2021; 4:1675-1688. [PMID: 34608449 PMCID: PMC8482323 DOI: 10.1021/acsptsci.1c00176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 11/30/2022]
Abstract
The National Center for Advancing Translational Sciences (NCATS) has been actively generating SARS-CoV-2 high-throughput screening data and disseminates it through the OpenData Portal (https://opendata.ncats.nih.gov/covid19/). Here, we provide a hybrid approach that utilizes NCATS screening data from the SARS-CoV-2 cytopathic effect reduction assay to build predictive models, using both machine learning and pharmacophore-based modeling. Optimized models were used to perform two iterative rounds of virtual screening to predict small molecules active against SARS-CoV-2. Experimental testing with live virus provided 100 (∼16% of predicted hits) active compounds (efficacy > 30%, IC50 ≤ 15 μM). Systematic clustering analysis of active compounds revealed three promising chemotypes which have not been previously identified as inhibitors of SARS-CoV-2 infection. Further investigation resulted in the identification of allosteric binders to host receptor angiotensin-converting enzyme 2; these compounds were then shown to inhibit the entry of pseudoparticles bearing spike protein of wild-type SARS-CoV-2, as well as South African B.1.351 and UK B.1.1.7 variants.
Collapse
Affiliation(s)
- Sankalp Jain
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel C. Talley
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bolormaa Baljinnyam
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jun Choe
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Quinlin Hanson
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Wei Zhu
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Miao Xu
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Catherine Z. Chen
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Wei Zheng
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Min Shen
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ganesha Rai
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Alexey V. Zakharov
- National Center for Advancing
Translational Sciences (NCATS), National
Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| |
Collapse
|
31
|
Mignani S, Shi X, Karpus A, Lentini G, Majoral JP. Functionalized Dendrimer Platforms as a New Forefront Arsenal Targeting SARS-CoV-2: An Opportunity. Pharmaceutics 2021; 13:1513. [PMID: 34575589 PMCID: PMC8466088 DOI: 10.3390/pharmaceutics13091513] [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: 08/27/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022] Open
Abstract
The novel human coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has caused a pandemic. There are currently several marketed vaccines and many in clinical trials targeting SARS-CoV-2. Another strategy is to repurpose approved drugs to decrease the burden of the COVID-19 (official name for the coronavirus disease) pandemic. as the FDA (U.S. Food and Drug Administration) approved antiviral drugs and anti-inflammatory drugs to arrest the cytokine storm, inducing the production of pro-inflammatory cytokines. Another view to solve these unprecedented challenges is to analyze the diverse nanotechnological approaches which are able to improve the COVID-19 pandemic. In this original minireview, as promising candidates we analyze the opportunity to develop biocompatible dendrimers as drugs themselves or as nanocarriers against COVID-19 disease. From the standpoint of COVID-19, we suggest developing dendrimers as shields against COVID-19 infection based on their capacity to be incorporated in several environments outside the patients and as important means to stop transmission of SARS-CoV-2.
Collapse
Affiliation(s)
- Serge Mignani
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR 860, 75006 Paris, France
- CQM—Centro de Química da Madeira, MMRG, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
| | - Xiangyang Shi
- CQM—Centro de Química da Madeira, MMRG, Campus da Penteada, Universidade da Madeira, 9020-105 Funchal, Portugal
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Andrii Karpus
- Laboratoire de Chimie de Coordination du CNRS, 205 Route de Narbonne, CEDEX 4, 31077 Toulouse, France;
- Université Toulouse 118 Route de Narbonne, CEDEX 4, 31077 Toulouse, France
| | - Giovanni Lentini
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy;
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 Route de Narbonne, CEDEX 4, 31077 Toulouse, France;
- Université Toulouse 118 Route de Narbonne, CEDEX 4, 31077 Toulouse, France
| |
Collapse
|
32
|
Mamontov E, Cheng Y, Daemen LL, Kolesnikov AI, Ramirez-Cuesta AJ, Ryder MR, Stone MB. Low rotational barriers for the most dynamically active methyl groups in the proposed antiviral drugs for treatment of SARS-CoV-2, apilimod and tetrandrine. Chem Phys Lett 2021; 777:138727. [PMID: 33994552 PMCID: PMC8105138 DOI: 10.1016/j.cplett.2021.138727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/30/2022]
Abstract
A recent screening study highlighted a molecular compound, apilimod, for its efficacy against the SARS-CoV-2 virus, while another compound, tetrandrine, demonstrated a remarkable synergy with the benchmark antiviral drug, remdesivir. Here, we find that because of significantly reduced potential energy barriers, which also give rise to pronounced quantum effects, the rotational dynamics of the most dynamically active methyl groups in apilimod and tetrandrine are much faster than those in remdesivir. Because dynamics of methyl groups are essential for biochemical activity, screening studies based on the computed potential energy profiles may help identify promising candidates within a given class of drugs.
Collapse
Affiliation(s)
- Eugene Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yongqiang Cheng
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Luke L Daemen
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | | | - Matthew R Ryder
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew B Stone
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
33
|
Vargas D, Larghi EL, Kaufman TS. Evolution of the Synthesis of Remdesivir. Classical Approaches and Most Recent Advances. ACS OMEGA 2021; 6:19356-19363. [PMID: 34368522 PMCID: PMC8340098 DOI: 10.1021/acsomega.1c03082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The broad-spectrum antiviral Remdesivir, a monophosphate nucleoside analogue prodrug (ProTide), was repurposed. In May 2020, it received emergency approval by the FDA, being the first drug approved to fight the new coronavirus (COVID-19) disease which targets the virus directly. The main synthetic strategies toward Remdesivir, and their relevant modifications, are presented and discussed, to provide a panoramic view of the state-of-the-art and the more important advances in this field. Recent progress, proposed improvements, and uses of novel technologies for the synthetic sequence are also detailed.
Collapse
Affiliation(s)
- Didier
F. Vargas
- Instituto de Química Rosario
(IQUIR, CONICET-UNR) and National University of Rosario (UNR), Suipacha 531, 2000 Rosario, Argentina
| | - Enrique L. Larghi
- Instituto de Química Rosario
(IQUIR, CONICET-UNR) and National University of Rosario (UNR), Suipacha 531, 2000 Rosario, Argentina
| | - Teodoro S. Kaufman
- Instituto de Química Rosario
(IQUIR, CONICET-UNR) and National University of Rosario (UNR), Suipacha 531, 2000 Rosario, Argentina
| |
Collapse
|
34
|
Dampalla CS, Zheng J, Perera KD, Wong LYR, Meyerholz DK, Nguyen HN, Kashipathy MM, Battaile KP, Lovell S, Kim Y, Perlman S, Groutas WC, Chang KO. Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2021; 118:e2101555118. [PMID: 34210738 PMCID: PMC8307543 DOI: 10.1073/pnas.2101555118] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to be a serious global public health threat. The 3C-like protease (3CLpro) is a virus protease encoded by SARS-CoV-2, which is essential for virus replication. We have previously reported a series of small-molecule 3CLpro inhibitors effective for inhibiting replication of human coronaviruses including SARS-CoV-2 in cell culture and in animal models. Here we generated a series of deuterated variants of a 3CLpro inhibitor, GC376, and evaluated the antiviral effect against SARS-CoV-2. The deuterated GC376 displayed potent inhibitory activity against SARS-CoV-2 in the enzyme- and the cell-based assays. The K18-hACE2 mice develop mild to lethal infection commensurate with SARS-CoV-2 challenge doses and were proposed as a model for efficacy testing of antiviral agents. We treated lethally infected mice with a deuterated derivative of GC376. Treatment of K18-hACE2 mice at 24 h postinfection with a derivative (compound 2) resulted in increased survival of mice compared to vehicle-treated mice. Lung virus titers were decreased, and histopathological changes were ameliorated in compound 2-treated mice compared to vehicle-treated mice. Structural investigation using high-resolution crystallography illuminated binding interactions of 3CLpro of SARS-CoV-2 and SARS-CoV with deuterated variants of GC376. Taken together, deuterated GC376 variants have excellent potential as antiviral agents against SARS-CoV-2.
Collapse
Affiliation(s)
| | - Jian Zheng
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242
| | - David K Meyerholz
- Department of Pathology, The University of Iowa, Iowa City, IA 52242
| | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, KS 67260
| | | | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506;
| | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242;
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260;
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506;
| |
Collapse
|
35
|
Preliminary investigation of drug impurities associated with the anti-influenza drug Favipiravir - An insilico approach. COMPUT THEOR CHEM 2021; 1204:113375. [PMID: 34306990 PMCID: PMC8285362 DOI: 10.1016/j.comptc.2021.113375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 01/08/2023]
Abstract
The role of repurposed or modified antiviral drugs has become more significant during the current global pandemic of SARS Covid-19. In the present study, four structurally analogous impurity molecules of antiviral drug Favipiravir are selected for preliminary computational investigation for assessing the structure-activity relationship. The optimized geometry and the electronic structures of the compounds are computed using Density Functional Theory as a precursor to evaluating their physical, chemical and spectral properties. The frontier orbitals analysis is performed to obtain global reactivity parameters namely, the chemical potential, absolute electronegativity, global softness, global hardness, electrophilicity, etc. The natural Bond Orbital (NBO) analysis and Mulliken analysis provided an understanding of the charge-transfer interactions of molecules. The possibilities of intermolecular interactions of the drug systems with the receptors are also visualized using the electrostatic potential maps (MEP) derived from the DFT computations. The physiochemical properties are assessed computationally using SwissADME webtool to correlate the structural aspects of the compounds with their biological responses. Useful parameters namely flexibility, lipophilicity, size, polarity, solubility and saturation were also computed to evaluate the therapeutic activity or drug-likeness.
Collapse
|
36
|
Mariewskaya KA, Tyurin AP, Chistov AA, Korshun VA, Alferova VA, Ustinov AV. Photosensitizing Antivirals. Molecules 2021; 26:3971. [PMID: 34209713 PMCID: PMC8271894 DOI: 10.3390/molecules26133971] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/22/2021] [Accepted: 06/27/2021] [Indexed: 12/23/2022] Open
Abstract
Antiviral action of various photosensitizers is already summarized in several comprehensive reviews, and various mechanisms have been proposed for it. However, a critical consideration of the matter of the area is complicated, since the exact mechanisms are very difficult to explore and clarify, and most publications are of an empirical and "phenomenological" nature, reporting a dependence of the antiviral action on illumination, or a correlation of activity with the photophysical properties of the substances. Of particular interest is substance-assisted photogeneration of highly reactive singlet oxygen (1O2). The damaging action of 1O2 on the lipids of the viral envelope can probably lead to a loss of the ability of the lipid bilayer of enveloped viruses to fuse with the lipid membrane of the host cell. Thus, lipid bilayer-affine 1O2 photosensitizers have prospects as broad-spectrum antivirals against enveloped viruses. In this short review, we want to point out the main types of antiviral photosensitizers with potential affinity to the lipid bilayer and summarize the data on new compounds over the past three years. Further understanding of the data in the field will spur a targeted search for substances with antiviral activity against enveloped viruses among photosensitizers able to bind to the lipid membranes.
Collapse
Affiliation(s)
- Kseniya A. Mariewskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (K.A.M.); (A.P.T.); (A.A.C.); (V.A.K.)
- Higher Chemical College of the Russian Academy of Sciences, Mendeleev University of Chemical Technology, Miusskaya sq. 9, 125047 Moscow, Russia
| | - Anton P. Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (K.A.M.); (A.P.T.); (A.A.C.); (V.A.K.)
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia
| | - Alexey A. Chistov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (K.A.M.); (A.P.T.); (A.A.C.); (V.A.K.)
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (K.A.M.); (A.P.T.); (A.A.C.); (V.A.K.)
| | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (K.A.M.); (A.P.T.); (A.A.C.); (V.A.K.)
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (K.A.M.); (A.P.T.); (A.A.C.); (V.A.K.)
| |
Collapse
|
37
|
Paul SS, Biswas G. Repurposed Antiviral Drugs for the Treatment of COVID-19: Syntheses, Mechanism of Infection and Clinical Trials. Mini Rev Med Chem 2021; 21:1123-1143. [PMID: 33355053 DOI: 10.2174/1389557521666201222145842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/22/2022]
Abstract
COVID-19 is a public health emergency of international concern. Although considerable knowledge has been acquired with time about the viral mechanism of infection and mode of replication, yet no specific drugs or vaccines have been discovered against SARS-CoV-2 to date. There are few small molecule antiviral drugs like Remdesivir and Favipiravir, which have shown promising results in different advanced stages of clinical trials. Chloroquinine, Hydroxychloroquine, and Lopinavir- Ritonavir combination, although initially were hypothesized to be effective against SARSCoV- 2, are now discontinued from the solidarity clinical trials. This review provides a brief description of their chemical syntheses along with their mode of action, and clinical trial results available on Google and in different peer-reviewed journals till 24th October 2020.
Collapse
Affiliation(s)
| | - Goutam Biswas
- Department of Chemistry, Cooch Behar Panchanan Barma University, Panchanan Nagar, Cooch Behar 736101, India
| |
Collapse
|
38
|
Carroll EL, Bailo M, Reihill JA, Crilly A, Lockhart JC, Litherland GJ, Lundy FT, McGarvey LP, Hollywood MA, Martin SL. Trypsin-Like Proteases and Their Role in Muco-Obstructive Lung Diseases. Int J Mol Sci 2021; 22:5817. [PMID: 34072295 PMCID: PMC8199346 DOI: 10.3390/ijms22115817] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Trypsin-like proteases (TLPs) belong to a family of serine enzymes with primary substrate specificities for the basic residues, lysine and arginine, in the P1 position. Whilst initially perceived as soluble enzymes that are extracellularly secreted, a number of novel TLPs that are anchored in the cell membrane have since been discovered. Muco-obstructive lung diseases (MucOLDs) are characterised by the accumulation of hyper-concentrated mucus in the small airways, leading to persistent inflammation, infection and dysregulated protease activity. Although neutrophilic serine proteases, particularly neutrophil elastase, have been implicated in the propagation of inflammation and local tissue destruction, it is likely that the serine TLPs also contribute to various disease-relevant processes given the roles that a number of these enzymes play in the activation of both the epithelial sodium channel (ENaC) and protease-activated receptor 2 (PAR2). More recently, significant attention has focused on the activation of viruses such as SARS-CoV-2 by host TLPs. The purpose of this review was to highlight key TLPs linked to the activation of ENaC and PAR2 and their association with airway dehydration and inflammatory signalling pathways, respectively. The role of TLPs in viral infectivity will also be discussed in the context of the inhibition of TLP activities and the potential of these proteases as therapeutic targets.
Collapse
Affiliation(s)
- Emma L. Carroll
- School of Pharmacy, Queen’s University, Belfast BT9 7BL, UK; (E.L.C.); (J.A.R.)
| | - Mariarca Bailo
- Institute for Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (M.B.); (A.C.); (J.C.L.); (G.J.L.)
| | - James A. Reihill
- School of Pharmacy, Queen’s University, Belfast BT9 7BL, UK; (E.L.C.); (J.A.R.)
| | - Anne Crilly
- Institute for Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (M.B.); (A.C.); (J.C.L.); (G.J.L.)
| | - John C. Lockhart
- Institute for Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (M.B.); (A.C.); (J.C.L.); (G.J.L.)
| | - Gary J. Litherland
- Institute for Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (M.B.); (A.C.); (J.C.L.); (G.J.L.)
| | - Fionnuala T. Lundy
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast BT9 7BL, UK; (F.T.L.); (L.P.M.)
| | - Lorcan P. McGarvey
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University, Belfast BT9 7BL, UK; (F.T.L.); (L.P.M.)
| | - Mark A. Hollywood
- Smooth Muscle Research Centre, Dundalk Institute of Technology, A91 HRK2 Dundalk, Ireland;
| | - S. Lorraine Martin
- School of Pharmacy, Queen’s University, Belfast BT9 7BL, UK; (E.L.C.); (J.A.R.)
| |
Collapse
|
39
|
Hughes DL. Quest for a Cure: Potential Small-Molecule Treatments for COVID-19, Part 2. Org Process Res Dev 2021; 25:1089-1111. [PMID: 37556259 PMCID: PMC8084274 DOI: 10.1021/acs.oprd.1c00100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 12/15/2022]
Abstract
During the first year of the outbreak of the COVID-19 pandemic, many drugs and drug candidates have been evaluated as treatment options. None yet has proved to be an effective cure, but progress in controlling the disease has been made. In June 2020 we published an article that described the mechanistic rationale behind the repurposing of seven licensed drugs in clinical trials for the treatment of COVID-19 and reviewed synthetic routes to these drugs. Several developments have occurred since then. Remdesivir (trade name Veklury) has been approved for use in the U.S. and Europe. Dexamethasone, a steroid drug first approved in 1959, has shown mortality reduction in severe COVID patients. Molnupiravir, a new and promising oral antiviral drug, is being studied in late-stage clinical trials. In this review, we update synthetic work that has been recently published on remdesivir, provide an overview of several routes to molnupiravir, and review classical routes to dexamethasone as well as some of those more recently developed.
Collapse
Affiliation(s)
- David L. Hughes
- sp3 Pharma Consulting, 6755 Mira Mesa Boulevard,
STE123-217, San Diego, California 92121, United States
| |
Collapse
|
40
|
Adhikari B, Sahu N. COVID-19 into Chemical Science Perspective: Chemical Preventive Measures and Drug Development. ChemistrySelect 2021; 6:2010-2028. [PMID: 33821213 PMCID: PMC8013609 DOI: 10.1002/slct.202100127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/12/2021] [Indexed: 01/08/2023]
Abstract
COVID-19 facts and literature are discussed into chemical science intuition highlighting the direct role of chemistry to the ongoing global pandemic by covering structural identification of the virus, chemical preventive measures and development of drugs. We reviewed the four most promising repurposed drugs which are presently being investigated in mass clinical trials on COVID-19 infected persons and synthetic routes of these drugs with their recent advancement. Chemical preventive measures such as soap water, hand sanitizer and disinfectant are the only available options in the arsenal to fight against COVID-19, till an effective medicine or vaccine will be made available. As such the present review will focus on the mode of action of the major chemical preventives.
Collapse
Affiliation(s)
- Bimalendu Adhikari
- Department of ChemistryNational Institute of Technology Rourkela RourkelaOdisha769008India
| | - Nihar Sahu
- Department of ChemistryNational Institute of Technology Rourkela RourkelaOdisha769008India
| |
Collapse
|
41
|
Shahcheraghi SH, Ayatollahi J, Aljabali AAA, Shastri MD, Shukla SD, Chellappan DK, Jha NK, Anand K, Katari NK, Mehta M, Satija S, Dureja H, Mishra V, Almutary AG, Alnuqaydan AM, Charbe N, Prasher P, Gupta G, Dua K, Lotfi M, Bakshi HA, Tambuwala MM. An overview of vaccine development for COVID-19. Ther Deliv 2021; 12:235-244. [PMID: 33624533 PMCID: PMC7923686 DOI: 10.4155/tde-2020-0129] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic continues to endanger world health and the economy. The causative SARS-CoV-2 coronavirus has a unique replication system. The end point of the COVID-19 pandemic is either herd immunity or widespread availability of an effective vaccine. Multiple candidate vaccines - peptide, virus-like particle, viral vectors (replicating and nonreplicating), nucleic acids (DNA or RNA), live attenuated virus, recombinant designed proteins and inactivated virus - are presently under various stages of expansion, and a small number of vaccine candidates have progressed into clinical phases. At the time of writing, three major pharmaceutical companies, namely Pfizer and Moderna, have their vaccines under mass production and administered to the public. This review aims to investigate the most critical vaccines developed for COVID-19 to date.
Collapse
Affiliation(s)
- Seyed H Shahcheraghi
- Infectious Diseases Research Center, Shahid Sadoughi Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Jamshid Ayatollahi
- Infectious Diseases Research Center, Shahid Sadoughi Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Alaa AA Aljabali
- Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid, Jordan
| | - Madhur D Shastri
- School of Pharmacy & Pharmacology, University of Tasmania, Hobart, Australia
| | - Shakti D Shukla
- Priority Research Centre for Healthy Lungs, School of Medicine & Public Health, The University of Newcastle, Callaghan, Australia
| | - Dinesh K Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Niraj K Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences & National Health Laboratory Service, University of the Free State, Bloemfontein, South Africa
| | - Naresh K Katari
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502329, India
| | - Meenu Mehta
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Saurabh Satija
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Harish Dureja
- Faculty of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, India
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Abdulmajeed G Almutary
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Saudi Arabia
| | - Abdullah M Alnuqaydan
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Saudi Arabia
| | - Nitin Charbe
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Av. Libertador Bernardo O’Higgins, Santiago 340, Región Metropolitana, Chile
| | - Parteek Prasher
- Department of Chemistry, University of Petroleum & Energy Studies, Dehradun 248007, India
| | - Gaurav Gupta
- School of Pharmaceutical Sciences, Suresh Gyan Vihar University, Jaipur, India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Marzieh Lotfi
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Abortion Research Center, Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hamid A Bakshi
- School of Pharmacy & Pharmaceutical Sciences, Ulster University, Coleraine, County Londonderry, Northern Ireland, BT52 1SA, UK
| | - Murtaza M Tambuwala
- School of Pharmacy & Pharmaceutical Sciences, Ulster University, Coleraine, County Londonderry, Northern Ireland, BT52 1SA, UK
| |
Collapse
|
42
|
Sarkar K, Das RK. Preliminary Identification of Hamamelitannin and Rosmarinic Acid as COVID-19 Inhibitors Based on Molecular Docking. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999200802032126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background:
Recently, novel coronavirus disease, COVID-19 caused the outbreak situation
of global public health. In this pandemic situation, all the people's lives of 212 Countries and
Territories have been affected due to partial or complete lockdown and also as a result of mandatory
isolations or quarantines. This is due to the non-availability of any secure vaccine.
Objective:
The present study helps us to identify and screen the best phytochemicals as potent inhibitors
against COVID-19.
Methods:
In this paper, we choose two standard drugs namely hamamelitannin and rosmarinic acid
as a probable inhibitor of pandemic COVID-19 receptor as compared to antimalarial drugs hydroxychloroquine,
anti-viral drug remdesivir, and also baricitinib. This study was done by taking
into consideration of molecular docking study, performed with Auto Dock 4.0 (AD4.0). All chemical
structures were optimized with the Avogadro suite by applying the MMFF94 force field and also
hamamelitannin, rosmarinic acid was optimized using the Gaussian G16 suite of UB3LYP/6-
311++G(d,p) basis set. Protein-ligand interaction was visualized by PyMOL software.
Results:
This work has provided an insightful understanding of protein-ligand interaction of hamamelitannin
and rosmarinic acid showing comparable binding energies than that of clinically applying
probable COVID-19 inhibitors hydroxychloroquine (an anti-malarial drug) and remdesivir (an
anti-viral drug).
Conclusions:
We will expect that if its anti-SARS-CoV-2 activity is validated in human clinical trials,
these two drugs may be developed as an effective antiviral therapeutics towards infected patients
in this outbreak and pandemic situation of COVID-19.
Collapse
Affiliation(s)
- Kaushik Sarkar
- Department of Chemistry, University of North Bengal, Darjeeling, West Bengal, India
| | - Rajesh Kumar Das
- Department of Chemistry, University of North Bengal, Darjeeling, West Bengal, India
| |
Collapse
|
43
|
Mehta PP, Dhapte-Pawar VS. Novel and Evolving Therapies for COVID-19 Related Pulmonary Complications . Am J Med Sci 2021; 361:557-566. [PMID: 33640363 PMCID: PMC7906517 DOI: 10.1016/j.amjms.2021.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/07/2020] [Accepted: 02/23/2021] [Indexed: 12/23/2022]
Abstract
Coronaviruses disease 2019 (COVID-19) is the most crucial threat, the world has ever witnessed. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of this disease pandemic. The World Health Organization has confirmed the continuing epidemic as a worldwide public health crisis. Presently, the research on COVID-19 is even in the primitive stage. Studies on unveiling the natural route of COVID-19 infection and related pathophysiology, the biology of pulmonary airways pose a more rational restorative approach in the management of COVID-19. Thus, based on the existing facts, we methodically reviewed the efforts put forth by various research institutes, pharmaceutical companies and biotechnology firms in pulmonary delivery to prevent and control the COVID-19. This article would be valuable for the healthcare community, which is efficiently dealing with the SARS-CoV-2 crisis.
Collapse
Affiliation(s)
- Piyush P Mehta
- Department of Quality Assurance Technique, Poona College of Pharmacy, Bharati Vidyapeeth University, Pune - 38, Maharashtra, India
| | - Vividha S Dhapte-Pawar
- Department of Pharmaceutics, Poona College of Pharmacy, Bharati Vidyapeeth University, Pune - 38, Maharashtra, India.
| |
Collapse
|
44
|
von Keutz T, Williams JD, Kappe CO. Flash Chemistry Approach to Organometallic C-Glycosylation for the Synthesis of Remdesivir. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Timo von Keutz
- Center for Continuous Flow Synthesis and Processing (CC FLOW), Research Center Pharmaceutical Engineering GmbH (RCPE), Inffeldgasse 13, 8010 Graz, Austria
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Jason D. Williams
- Center for Continuous Flow Synthesis and Processing (CC FLOW), Research Center Pharmaceutical Engineering GmbH (RCPE), Inffeldgasse 13, 8010 Graz, Austria
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - C. Oliver Kappe
- Center for Continuous Flow Synthesis and Processing (CC FLOW), Research Center Pharmaceutical Engineering GmbH (RCPE), Inffeldgasse 13, 8010 Graz, Austria
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
| |
Collapse
|
45
|
Tian D, Liu Y, Liang C, Xin L, Xie X, Zhang D, Wan M, Li H, Fu X, Liu H, Cao W. An update review of emerging small-molecule therapeutic options for COVID-19. Biomed Pharmacother 2021; 137:111313. [PMID: 33556871 PMCID: PMC7857046 DOI: 10.1016/j.biopha.2021.111313] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/16/2021] [Accepted: 01/21/2021] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 outbreak and pandemic that began near the end of 2019 has posed a challenge to global health. At present, many candidate small-molecule therapeutics have been developed that can inhibit both the infection and replication of SARS-CoV-2 and even potentially relieve cytokine storms and other related complications. Meanwhile, host-targeted drugs that inhibit cellular transmembrane serine protease (TMPRSS2) can prevent SARS-CoV-2 from entering cells, and its combination with chloroquine and dihydroorotate dehydrogenase (DHODH) inhibitors can limit the spread of SARS-CoV-2 and reduce the morbidity and mortality of patients with COVID-19. The present article provides an overview of these small-molecule therapeutics based on insights from medicinal chemistry research and focuses on RNA-dependent RNA polymerase (RdRp) inhibitors, such as the nucleoside analogues remdesivir, favipiravir and ribavirin. This review also covers inhibitors of 3C-like protease (3CLpro), papain-like protease (PLpro) and other potentially innovative active ingredient molecules, describing their potential targets, activities, clinical status and side effects.
Collapse
Affiliation(s)
- Dengke Tian
- School of Life Sciences, Jilin University, Changchun, 130012, PR China
| | - Yuzhi Liu
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Chengyuan Liang
- School of Life Sciences, Jilin University, Changchun, 130012, PR China; Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Liang Xin
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Dezhu Zhang
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Minge Wan
- School of Medicine and Pharmacy, Shaanxi University of Business & Commerce, Xi'an 712046, PR China
| | - Han Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Xueqi Fu
- School of Life Sciences, Jilin University, Changchun, 130012, PR China
| | - Hong Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai, 519030, PR China.
| | - Wenqiang Cao
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai, 519030, PR China.
| |
Collapse
|
46
|
Chugh H, Awasthi A, Agarwal Y, Gaur RK, Dhawan G, Chandra R. A comprehensive review on potential therapeutics interventions for COVID-19. Eur J Pharmacol 2021; 890:173741. [PMID: 33227287 PMCID: PMC7677683 DOI: 10.1016/j.ejphar.2020.173741] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/15/2022]
Abstract
COVID-19 is an infectious respiratory disease caused by SARS-CoV-2, a new beta coronavirus that emerged in Wuhan, China. Being primarily a respiratory disease, it is highly transmissible through both direct and indirect contacts. It displays a range of symptoms in different individuals and thus has been grouped into mild, moderate, and severe diseases. The virus utilizes spike proteins present on its surface to recognize ACE-2 receptors present on the host cells to enter the cell cytoplasm and replicate. The viral invasion of cells induces damage response, pyroptosis, infiltration of immune cells, expression of pro-inflammatory cytokines (cytokine storm), and activation of the adaptive immune system. Depending on viral load and host factors like age and underlying medical conditions, the immune responses mounted against SARS-CoV-2 may cause acute respiratory distress syndrome (ARDS), multiple organ failure, and death. In this review, we specify and justify both viral and host therapeutic targets that can be modulated to relieve the symptoms and treat the disease. Furthermore, we discuss vaccine development in the time of pandemic and the most promising vaccine candidates by far, according to WHO database. Finally, we discuss the conventional re-purposed drugs and potential alternative treatments as adjuvants.
Collapse
Affiliation(s)
- Heerak Chugh
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Amardeep Awasthi
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Yashi Agarwal
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Rajesh K Gaur
- Division of Medical Oncology, University of Southern California, CA 90033, USA
| | - Gagan Dhawan
- Department of Biomedical Sciences, Acharya Narendra Dev College, University of Delhi, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India; Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
47
|
Chugh H, Awasthi A, Agarwal Y, Gaur RK, Dhawan G, Chandra R. A comprehensive review on potential therapeutics interventions for COVID-19. Eur J Pharmacol 2021. [PMID: 33227287 DOI: 10.1016/j.ejphar.2020.17374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
COVID-19 is an infectious respiratory disease caused by SARS-CoV-2, a new beta coronavirus that emerged in Wuhan, China. Being primarily a respiratory disease, it is highly transmissible through both direct and indirect contacts. It displays a range of symptoms in different individuals and thus has been grouped into mild, moderate, and severe diseases. The virus utilizes spike proteins present on its surface to recognize ACE-2 receptors present on the host cells to enter the cell cytoplasm and replicate. The viral invasion of cells induces damage response, pyroptosis, infiltration of immune cells, expression of pro-inflammatory cytokines (cytokine storm), and activation of the adaptive immune system. Depending on viral load and host factors like age and underlying medical conditions, the immune responses mounted against SARS-CoV-2 may cause acute respiratory distress syndrome (ARDS), multiple organ failure, and death. In this review, we specify and justify both viral and host therapeutic targets that can be modulated to relieve the symptoms and treat the disease. Furthermore, we discuss vaccine development in the time of pandemic and the most promising vaccine candidates by far, according to WHO database. Finally, we discuss the conventional re-purposed drugs and potential alternative treatments as adjuvants.
Collapse
Affiliation(s)
- Heerak Chugh
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Amardeep Awasthi
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Yashi Agarwal
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Rajesh K Gaur
- Division of Medical Oncology, University of Southern California, CA 90033, USA
| | - Gagan Dhawan
- Department of Biomedical Sciences, Acharya Narendra Dev College, University of Delhi, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India; Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
48
|
Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
Collapse
Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| |
Collapse
|
49
|
Tiyasakulchai T, Charoensetakul N, Khamkhenshorngphanuch T, Thongpanchang C, Srikun O, Yuthavong Y, Srimongkolpithak N. Scalable synthesis of favipiravir via conventional and continuous flow chemistry. RSC Adv 2021; 11:38691-38693. [PMID: 35493228 PMCID: PMC9044180 DOI: 10.1039/d1ra06963b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
Decagram scale synthesis of favipiravir was performed in 9 steps using diethyl malonate as cheap starting material. Hydrogenation and bromination steps were achieved by employing a continuous flow reactor. The synthetic process provided a total of 16% yield and it is suitable for larger-scale synthesis and production. Decagram scale synthesis of favipiravir was performed in 9 steps using diethyl malonate as cheap starting material.![]()
Collapse
Affiliation(s)
- Thanat Tiyasakulchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Netnapa Charoensetakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | | - Chawanee Thongpanchang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Onsiri Srikun
- Government Pharmaceutical Organization (GPO), Bangkok, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nitipol Srimongkolpithak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| |
Collapse
|
50
|
Knapp R, Tona V, Okada T, Sarpong R, Garg NK. Cyanoamidine Cyclization Approach to Remdesivir's Nucleobase. Org Lett 2020; 22:8430-8435. [PMID: 33085486 PMCID: PMC7653677 DOI: 10.1021/acs.orglett.0c03052] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Indexed: 11/30/2022]
Abstract
We report an alternative approach to the unnatural nucleobase fragment seen in remdesivir (Veklury). Remdesivir displays broad-spectrum antiviral activity and is currently being evaluated in Phase III clinical trials to treat patients with COVID-19. Our route relies on the formation of a cyanoamidine intermediate, which undergoes Lewis acid-mediated cyclization to yield the desired nucleobase. The approach is strategically distinct from prior routes and could further enable the synthesis of remdesivir and other small-molecule therapeutics.
Collapse
Affiliation(s)
- Rachel
R. Knapp
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Veronica Tona
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Taku Okada
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Richmond Sarpong
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Neil K. Garg
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| |
Collapse
|