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1.
Letters in Applied NanoBioScience ; 11(4):4201-4212, 2022.
Article in English | Scopus | ID: covidwho-2303454

ABSTRACT

Novel coronavirus (COVID-19) recently emerged as a new pandemic disease that affects millions of people worldwide. This disease considers as a potential threat to human society. Researchers are continuously working to identify virus structure, the pathophysiology of the disease, and possible treatment of the disease. Currently, to fight against the coronavirus, two major strategies have been adopted throughout the world;one is to target virus-cell machinery, and the second is to improve patient immunity. In this review, we have described detailed information about the structure and life cycle of the novel coronavirus, current therapy, and future strategies to fight against this pandemic disease. Computational methods are useful for understanding virus structure, disease pathology, and discovering novel anti-COVID agents. These methods can provide fast and efficient solutions to fight against this disease. We also highlighted the potential role of robotic technology and its importance in various clinical aspects. These robotic technologies may also play an important role in fighting COVID-19. © 2021 by the authors.

2.
Fused Pyrimidine-Based Drug Discovery ; : 117-164, 2022.
Article in English | Scopus | ID: covidwho-2267468

ABSTRACT

Pyrimidines-based drugs are one of the most important drugs for novel and recurring viruses, including the coronavirus. This chapter deals with 41 FDA-approved five-membered ring fused pyrimidine-based drugs, their synthetic strategies, and pharmacological activities. © 2023 Elsevier Ltd. All rights reserved.

3.
Coronaviruses ; 1(1):98-107, 2020.
Article in English | EMBASE | ID: covidwho-2281800

ABSTRACT

Background: Spread of COVID-19 attains a crucial transition in reveling its pandemic across the boundaries. In combating the infection caused by SARS-CoV-2, there is a spectrum of ideal strategies that have been adopted globally, of which repurposing of approved drugs considerably having high clinical relevance. 3-chymotrypsin-like protease (3CL pro) is considered to be the potential target for the researchers as it is highly essential for cleavage of polyprotein to get 16 nonstructural proteins (called nsp1-nsp16). These proteins are highly essential for viral replication and hence become a primary target for enzyme inhibitors. 3CL pro, having a structural projectile helical chain with biologically active site involved in processing viral polyproteins that are evolved from RNA genome translation. Objective(s): The major objective of the present investigation is to evaluate the enzyme inhibition potential of FDA approved therapeutic leads in targeting 3CLpro that medicates the viral replication. Method(s): Docking calculations were carried out for an array of FDA approved molecules which leads to a notable few molecules such as Emtricitabine, Oseltamivir, Ganciclovir, Chloroquine, Baricitinib, Favipiravir, Lopinavir, Ritonavir, Remdesivir, Ribavirin, Tenofovir, Umifenovir, Carbapenam, Ertap-enem and Imipenam which have both specificity and selectivity in terms of binding efficiency against 3CL proenzyme. Result(s): A combinatorial evaluation employing in-silico screening shows a major lead for remdesivir which possesses a substantial affinity to 3CL pro binding on core amino acid residues, such as Leu 27, His 41, Gly 143, Cys 145, His 164, Met 165, Glu 166, Pro 168 and His 172 which share the biological significance in mediating enzymatic action. Results of docking simulation by Autodock over a host of FDA approved molecules show high degree of selectivity and specificity in the increasing order of binding capacity;Remdesivir> Ertapenem> Imipenam> Tenofovir> Umifenovir> Chloroquine> Lopinavir> Ritonavir> Emtricitabine> Ganciclovir> Baricitinib> Ribavirin>Oseltamivir>Favipiravir> Carbapenam. Conclusion(s): Till date, there is no known cure attained for treating COVID-19 infection. In conclusion, lead molecules from already approved sources provoke promising potential which grabs the attention of the clinicians in availing potential therapeutic candidate as a drug of choice in the clinical management of COVID-19 time-dependently.Copyright © 2020 Bentham Science Publishers.

4.
J Biomol Struct Dyn ; : 1-17, 2021 Nov 16.
Article in English | MEDLINE | ID: covidwho-2257032

ABSTRACT

COVID-19, for which no confirmed therapeutic agents are available, has claimed over 48,14,000 lives globally. A feasible and quicker method to resolve this problem may be 'drug repositioning'. We investigated selected FDA and WHO-EML approved drugs based on their previously promising potential as antivirals, antibacterials or antifungals. These drugs were docked onto the nsp12 protein, which reigns the RNA-dependent RNA polymerase activity of SARS-CoV-2, a key therapeutic target for coronaviruses. Docked complexes were reevaluated using MM-GBSA analysis and the top three inhibitor-protein complexes were subjected to 100 ns long molecular dynamics simulation followed by another round of MM-GBSA analysis. The RMSF plots, binding energies and the mode of physicochemical interaction of the active site of the protein with the drugs were evaluated. Suramin, Penciclovir, and Anidulafungin were found to bind to nsp12 with similar binding energies as that of Remdesivir, which has been used as a therapy for COVID-19. In addition, recent experimental evidences indicate that these drugs exhibit antiviral efficacy against SARS-CoV-2. Such evidence, along with the significant and varied physical interactions of these drugs with the key viral enzyme outlined in this investigation, indicates that they might have a prospective therapeutic potential in the treatment of COVID-19 as monotherapy or combination therapy with Remdesivir.

5.
Front Mol Biosci ; 10: 1133123, 2023.
Article in English | MEDLINE | ID: covidwho-2278924

ABSTRACT

The COVID-19 pandemic caused by SARS-CoV-2 has caused millions of infections and deaths worldwide. Limited treatment options and the threat from emerging variants underline the need for novel and widely accessible therapeutics. G-quadruplexes (G4s) are nucleic acid secondary structures known to affect many cellular processes including viral replication and transcription. We identified heretofore not reported G4s with remarkably low mutation frequency across >5 million SARS-CoV-2 genomes. The G4 structure was targeted using FDA-approved drugs that can bind G4s - Chlorpromazine (CPZ) and Prochlorperazine (PCZ). We found significant inhibition in lung pathology and lung viral load of SARS-CoV-2 challenged hamsters when treated with CPZ or PCZ that was comparable to the widely used antiviral drug Remdesivir. In support, in vitro G4 binding, inhibition of reverse transcription from RNA isolated from COVID-infected humans, and attenuated viral replication and infectivity in Vero cell cultures were clear in case of both CPZ and PCZ. Apart from the wide accessibility of CPZ/PCZ, targeting relatively invariant nucleic acid structures poses an attractive strategy against viruses like SARS-CoV-2, which spread fast and accumulate mutations quickly.

6.
Viruses ; 15(3)2023 03 07.
Article in English | MEDLINE | ID: covidwho-2269941

ABSTRACT

Viral vectors have been used for a broad spectrum of gene therapy for both acute and chronic diseases. In the context of cancer gene therapy, viral vectors expressing anti-tumor, toxic, suicide and immunostimulatory genes, such as cytokines and chemokines, have been applied. Oncolytic viruses, which specifically replicate in and kill tumor cells, have provided tumor eradication, and even cure of cancers in animal models. In a broader meaning, vaccine development against infectious diseases and various cancers has been considered as a type of gene therapy. Especially in the case of COVID-19 vaccines, adenovirus-based vaccines such as ChAdOx1 nCoV-19 and Ad26.COV2.S have demonstrated excellent safety and vaccine efficacy in clinical trials, leading to Emergency Use Authorization in many countries. Viral vectors have shown great promise in the treatment of chronic diseases such as severe combined immunodeficiency (SCID), muscular dystrophy, hemophilia, ß-thalassemia, and sickle cell disease (SCD). Proof-of-concept has been established in preclinical studies in various animal models. Clinical gene therapy trials have confirmed good safety, tolerability, and therapeutic efficacy. Viral-based drugs have been approved for cancer, hematological, metabolic, neurological, and ophthalmological diseases as well as for vaccines. For example, the adenovirus-based drug Gendicine® for non-small-cell lung cancer, the reovirus-based drug Reolysin® for ovarian cancer, the oncolytic HSV T-VEC for melanoma, lentivirus-based treatment of ADA-SCID disease, and the rhabdovirus-based vaccine Ervebo against Ebola virus disease have been approved for human use.


Subject(s)
Genetic Therapy , Genetic Vectors , Animals , Humans , Ad26COVS1 , Carcinoma, Non-Small-Cell Lung , ChAdOx1 nCoV-19 , Genetic Vectors/genetics , Lung Neoplasms
7.
Med Drug Discov ; : 100148, 2022 Nov 29.
Article in English | MEDLINE | ID: covidwho-2240856

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) induced cytokine storm is the major cause of COVID­19 related deaths. Patients have been treated with drugs that work by inhibiting a specific protein partly responsible for the cytokines production. This approach provided very limited success, since there are multiple proteins involved in the complex cell signaling disease mechanisms. We targeted five proteins: Angiotensin II receptor type 1 (AT1R), A disintegrin and metalloprotease 17 (ADAM17), Nuclear Factor­Kappa B (NF­κB), Janus kinase 1 (JAK1) and Signal Transducer and Activator of Transcription 3 (STAT3), which are involved in the SARS­CoV­2 induced cytokine storm pathway. We developed machine learning (ML) models for these five proteins, using known active inhibitors. After developing the model for each of these proteins, FDA-approved drugs were screened to find novel therapeutics for COVID­19. We identified twenty drugs that are active for four proteins with predicted scores greater than 0.8 and eight drugs active for all five proteins with predicted scores over 0.85. Mitomycin C is the most active drug across all five proteins with an average prediction score of 0.886. For further validation of these results, we used the PyRx software to conduct protein-ligand docking experiments and calculated the binding affinity. The docking results support findings by the ML model. This research study predicted that several drugs can target multiple proteins simultaneously in cytokine storm-related pathway. These may be useful drugs to treat patients because these therapies can fight cytokine storm caused by the virus at multiple points of inhibition, leading to synergistically effective treatments.

8.
Curr Gene Ther ; 2022 Sep 21.
Article in English | MEDLINE | ID: covidwho-2232771

ABSTRACT

Viral vectors have proven useful in a broad spectrum of gene therapy applications due to their possibility to accommodate foreign genetic material for both local and systemic delivery. The wide range of viral vectors has enabled gene therapy applications for both acute and chronic diseases. Cancer gene therapy has been addressed by delivery of viral vectors expressing anti-tumor, toxic, and suicide genes for destruction of tumors. Delivery if immunostimulatory genes such as cytokines and chemokines has also been applied for cancer therapy. Moreover, oncolytic viruses specifically replicating in and killing tumor cells have been used as such for tumor eradication or in combination with tumor killing or immunostimulatory genes. In a broad meaning, vaccines against infectious diseases and various cancers can be considered as gene therapy, which has been highly successful not the least for development of effective COVID-19 vaccines. Viral vector-based gene therapy has also demonstrated encouraging and promising results for chronic diseases such as severe combined immunodeficiency (SCID), muscular dystrophy, and hemophilia. Preclinical gene therapy studies in animal models have demonstrated proof-of-concept for a wide range of disease indications. Clinical evaluation of drugs and vaccines in humans has showed high safety levels, good tolerance, and therapeutic efficacy. Several gene therapy drugs such as the adenovirus-based drug Gendicine® for non-small-cell lung cancer, the reovirus-based drug Reolysin® for ovarian cancer, lentivirus-based treatment of SCID-X1 disease, and the rhabdovirus-based vaccine Ervebo against Ebola virus disease, and adenovirus-based vaccines against COVID-19 have been developed.

9.
Indian J Pharmacol ; 54(6): 431-442, 2022.
Article in English | MEDLINE | ID: covidwho-2225962

ABSTRACT

INTRODUCTION: Binding of linoleic acid (LA) to the spike trimer stabilizes it in closed conformation hindering its binding to angiotensin-converting enzyme-2, thus decreasing infectivity. In the current study, we tend to repurpose Food and Drug Administration-approved drugs as binder to the LA binding pocket in wild and double mutant spike protein. MATERIALS AND METHODS: Approved drugs from DrugBank database (n = 2456) were prepared using Ligprep module of Schrodinger. Crystal structure of LA bound to spike trimer was retrieved (PDB: 6ZB4) and prepared using protein preparation wizard and grid was generated. A virtual screening was performed. With the help of molecular dynamics (MD) studies interaction profile of screened drugs were further evaluated. The selected hits were further evaluated for binding to the double mutant form of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). RESULTS AND DISCUSSION: Following virtual screening, a total of 26 molecules were shortlisted, which were further evaluated using 1ns MD simulation study. Four ligands showing better root mean square deviation (RMSD), RMSD to LA with interaction profile similar to LA were further evaluated using 100 ns MD simulation studies. A total of 2 hits were identified, which performed better than LA (selexipag and pralatrexate). Both these ligands were also found to bind to LA binding site of the double mutant form (E484Q and L452R); however, the binding affinity of pralatrexate was found to be better. CONCLUSION: We have identified 2 ligands (selexipag and pralatrexate) as possible stable binders to the LA binding site in spike trimer (wild and mutant form). Among them, pralatrexate has shown in vitro activity against SARS-CoV-2, validating our study results.


Subject(s)
Antiviral Agents , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Binding Sites , Ligands , Linoleic Acid , Molecular Dynamics Simulation , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Antiviral Agents/chemistry , Antiviral Agents/pharmacology
10.
Coronavirus Drug Discovery: Druggable Targets and In Silico Update: Volume 3 ; : 273-297, 2022.
Article in English | Scopus | ID: covidwho-2149161

ABSTRACT

In December 2019, the outbreak of acute respiratory illness caused by a novel coronavirus (2019-nCoV) keeps spreading at a rapid pace around the world. Lack of an effective vaccine, repurposing inhibitors, or de novo drug design might provide a long-term plan to combat this and potential infections due to specific virus conditions. The emergence of highly contagious COVID-19 and its high mortality rate among human populations has recently been declared a deadly pandemic that has provoked economic chaos and severe health problems. SARS-CoV-2 is an essential virus within its proteome, with several druggable components. The disease is a worldwide health issue that is instigated by severe acute coronavirus-2 syndrome (SARS-CoV-2) in the respiratory system. It is therefore of interest to research the binding features of 1615 drugs with FDA approval on the newly discovered main protease structure of 2019 novel coronavirus having strong sequence homology to that of SARS-CoV. © 2022 Elsevier Inc. All rights reserved.

11.
Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV2 Infection: Revolutionary Strategies to Combat Pandemics ; : 421-449, 2022.
Article in English | Scopus | ID: covidwho-2149130

ABSTRACT

The novel Coronavirus (nCoV), severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2), has shaken the whole world and posed significant challenges to the global healthcare system for more than a year. The scientific community across the globe is trying to combat this virus by developing a safe vaccine that can provide long-term immunity against the virus. The other means of overcoming its pathogenicity is to treat the infected people with available drugs and/or novel therapeutic strategies. The available drugs were previously designed to combat viral infections and come with tested safety. This appears to be the most practical approach as a quick response to the highly infectious pandemic with high morbidity and mortality. Although many repurposed drugs like favipiravir and hydroxychloroquine have been tried, they have been proven toxic and/or less efficacious. This has led the world to find urgent therapeutic interventions (traditional and novel), to help decrease the severity of COVID-19 infection and aim towards recovery. This chapter of the book will discuss the most up-to-date published data with respect to prevention and treatment of COVID-19 infection. Diagnosis also plays an important part in controlling the pandemic caused by the virus. A cheap, accurate and fast identification test for the virus is the need of the hour. This chapter will also throw light on the various diagnostic procedures available for the identification of SARS-CoV-2, till date, along with their advantages and disadvantages. © 2022 Elsevier Inc. All rights reserved.

12.
Current Bioinformatics ; 17(7):632-656, 2022.
Article in English | EMBASE | ID: covidwho-2141264

ABSTRACT

Background: RNA-dependent RNA polymerase (RdRp) contributes to the transcription cycle of the SARS-CoV-2 virus with the possible assistance of nsp-7-8 cofactors. Objective(s): The study aims to investigate the viral protective effects of complementary drugs in computational approaches that use viral proteins. Method(s): For the in silico studies, the identified compounds were subjected to molecular docking with RdRp protein followed by structural and functional analyses, density functional theory (DFT), and molecular dynamics (MD) simulation. The 3D structure of RdRp (6m71 PDB ID) was obtained from the protein databank as a target receptor. After reviewing the literature, 20 complementary and synthetic drugs were selected for docking studies. The top compounds were used for DFT and MD simulation at 200 ns. DFT of the compounds was calculated at B3LYP/6-311G (d, p) based on chemical properties, polarizability, and first-order hyperpolarizability. Results were analyzed using USCF Chimera, Discovery Studio, LigPlot, admetSAR, and mCule. Result(s): Computational studies confirmed the potent interaction of the complementary drugs forsythi-aside A, rhoifolin, and pectolinarin with RdRp. Common potential residues of RdRp (i.e., Thr-556, Tyr-619, Lys-621, Arg-624, Asn-691, and Asp-760) were observed for all three docking complexes with hydrogen bonding. Docking analysis showed strong key interactions, hydrogen bonding, and binding affinities (-8.4 to -8.5 kcal/mol) for these ligands over the FDA-approved drugs (-7.4 to -7.6 kcal/mol). Docking and simulation studies showed these residues in the binding domains. Conclusion(s): Significant outcomes of novel molecular interactions in docking, simulation, DFT, and binding domains in the structural and functional analyses of RdRp were observed. Copyright © 2022 Bentham Science Publishers.

13.
Biomolecules ; 12(12)2022 11 25.
Article in English | MEDLINE | ID: covidwho-2123517

ABSTRACT

The recent global health emergency caused by the coronavirus disease 2019 (COVID-19) pandemic has taken a heavy toll, both in terms of lives and economies. Vaccines against the disease have been developed, but the efficiency of vaccination campaigns worldwide has been variable due to challenges regarding production, logistics, distribution and vaccine hesitancy. Furthermore, vaccines are less effective against new variants of the SARS-CoV-2 virus and vaccination-induced immunity fades over time. These challenges and the vaccines' ineffectiveness for the infected population necessitate improved treatment options, including the inhibition of the SARS-CoV-2 main protease (Mpro). Drug repurposing to achieve inhibition could provide an immediate solution for disease management. Here, we used structure-based virtual screening (SBVS) to identify natural products (from NP-lib) and FDA-approved drugs (from e-Drug3D-lib and Drugs-lib) which bind to the Mpro active site with high-affinity and therefore could be designated as potential inhibitors. We prioritized nine candidate inhibitors (e-Drug3D-lib: Ciclesonide, Losartan and Telmisartan; Drugs-lib: Flezelastine, Hesperidin and Niceverine; NP-lib: three natural products) and predicted their half maximum inhibitory concentration using DeepPurpose, a deep learning tool for drug-target interactions. Finally, we experimentally validated Losartan and two of the natural products as in vitro Mpro inhibitors, using a bioluminescence resonance energy transfer (BRET)-based Mpro sensor. Our study suggests that existing drugs and natural products could be explored for the treatment of COVID-19.


Subject(s)
Antiviral Agents , Biological Products , COVID-19 , Coronavirus 3C Proteases , Coronavirus Protease Inhibitors , SARS-CoV-2 , Humans , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Biological Products/chemistry , Biological Products/pharmacology , Losartan/chemistry , Losartan/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Coronavirus Protease Inhibitors/chemistry , Coronavirus Protease Inhibitors/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors
14.
Biomedicines ; 10(11)2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2099347

ABSTRACT

The vaccine weapon has resulted in being essential in fighting the COVID-19 outbreak, but it is not fully preventing infection due to an alarming spreading of several identified variants of concern. In fact, the recent emergence of variants has pointed out how the SARS-CoV-2 pandemic still represents a global health threat. Moreover, oral antivirals also develop resistance, supporting the need to find new targets as therapeutic tools. However, cocktail therapy is useful to reduce drug resistance and maximize vaccination efficacy. Natural products and metal-drug-based treatments have also shown interesting antiviral activity, representing a valid contribution to counter COVID-19 outbreak. This report summarizes the available evidence which supports the use of approved drugs and further focuses on significant clinical trials that have investigated the safety and efficacy of repurposing drugs and new molecules in different COVID-19 phenotypes. To date, there are many individuals vulnerable to COVID-19 exhibiting severe symptoms, thus characterizing valid therapeutic strategies for better management of the disease is still a challenge.

15.
Pathogens ; 11(10)2022 Oct 18.
Article in English | MEDLINE | ID: covidwho-2082003

ABSTRACT

COVID-19, which emerged in December 2019, was declared a global pandemic by the World Health Organization (WHO) in March 2020. The disease was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has caused millions of deaths worldwide and caused social and economic disruption. While clinical trials on therapeutic drugs are going on in an Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) public-private partnership collaboration, current therapeutic approaches and options to counter COVID-19 remain few. Therapeutic drugs include the FDA-approved antiviral drugs, Remdesivir, and an immune modulator, Baricitinib. Hence, therapeutic approaches and alternatives for COVID-19 treatment need to be broadened. This paper discusses efforts in approaches to find treatment for COVID-19, such as inhibiting viral entry and disrupting the virus life cycle, and highlights the gap that needs to be filled in these approaches.

16.
Fused Pyrimidine-Based Drug Discovery ; : 117-164, 2023.
Article in English | ScienceDirect | ID: covidwho-2068597

ABSTRACT

Pyrimidines-based drugs are one of the most important drugs for novel and recurring viruses, including the coronavirus. This chapter deals with 41 FDA-approved five-membered ring fused pyrimidine-based drugs, their synthetic strategies, and pharmacological activities.

17.
Coronavirus Drug Discovery: Volume 1: SARS-CoV-2 (COVID-19) Prevention, Diagnosis, and Treatment ; : 249-264, 2022.
Article in English | Scopus | ID: covidwho-2048778

ABSTRACT

Coronavirus disease is a highly infectious disease caused by the 2019 novel coronavirus, now recognized as severe acute respiratory syndrome coronavirus 2. This pandemic caused great stress in the general public and led to the collapse of healthcare system in some places. Till date, there has not been an effective vaccine or antiviral drug for its treatment. As at the time of write-up, scientists, researchers, and industries in different countries are working collaboratively to develop an effective therapy or alternative to combat this deadly and highly infectious virus. To combat or overcome these difficulties, the United States Food and Drug Administration launched an FDA Coronavirus Treatment Acceleration Program (CTAP) to accelerate the development of new investigational drugs, biological therapies, vaccines, and medical devices for the treatment of COVID-19 patients. This chapter provides details about this, the role of FDA CTAP and the drugs they are evaluating for the treatment of this disease. © 2022 Elsevier Inc. All rights reserved.

18.
J Biomol Struct Dyn ; 40(2): 685-695, 2022 02.
Article in English | MEDLINE | ID: covidwho-1721854

ABSTRACT

3CLpro is the main protease of the novel coronavirus (SARS-CoV-2) responsible for their intracellular duplication. Based on virtual screening technology and molecular dynamics simulation, we found 23 approved clinical drugs such as Viomycin, Capastat, Carfilzomib and Saquinavir, which showed high affinity with the 3CLpro active sites. These findings showed that there were potential drugs that inhibit SARS-Cov-2's 3CLpro in the current clinical drug library, and these drugs can be further tested or chemically modified for the treatment of COVID-19.Communicated by Ramaswamy H. Sarma.


Subject(s)
COVID-19 , Pharmaceutical Preparations , Humans , Molecular Docking Simulation , Peptide Hydrolases , Protease Inhibitors/pharmacology , SARS-CoV-2
19.
Comput Biol Med ; 142: 105183, 2022 03.
Article in English | MEDLINE | ID: covidwho-1588024

ABSTRACT

With numerous infections and fatalities, COVID-19 has wreaked havoc around the globe. The main protease (Mpro), which cleaves the polyprotein to form non-structural proteins, thereby helping in the replication of SARS-CoV-2, appears as an attractive target for antiviral therapeutics. As FDA-approved drugs have shown effectiveness in targeting Mpro in previous SARS-CoV(s), molecular docking and virtual screening of existing antiviral, antimalarial, and protease inhibitor drugs were carried out against SARS-CoV-2 Mpro. Among 53 shortlisted drugs with binding energies lower than that of the crystal-bound inhibitor α-ketoamide 13 b (-6.7 kcal/mol), velpatasvir, glecaprevir, grazoprevir, baloxavir marboxil, danoprevir, nelfinavir, and indinavir (-9.1 to -7.5 kcal/mol) were the most significant on the list (hereafter referred to as the 53-list). Molecular dynamics (MD) simulations confirmed the stability of their Mpro complexes, with the MMPBSA binding free energy (ΔGbind) ranging between -124 kJ/mol (glecaprevir) and -28.2 kJ/mol (velpatasvir). Despite having the lowest initial binding energy, velpatasvir exhibited the highest ΔGbind value for escaping the catalytic site during the MD simulations, indicating its reduced efficacy, as observed experimentally. Available inhibition assay data adequately substantiated the computational forecast. Glecaprevir and nelfinavir (ΔGbind = -95.4 kJ/mol) appear to be the most effective antiviral drugs against Mpro. Furthermore, the remaining FDA drugs on the 53-list can be worth considering, since some have already demonstrated antiviral activity against SARS-CoV-2. Hence, theoretical pKi (Ki = inhibitor constant) values for all 53 drugs were provided. Notably, ΔGbind directly correlates with the average distance of the drugs from the His41-Cys145 catalytic dyad of Mpro, providing a roadmap for rapid screening and improving the inhibitor design against SARS-CoV-2 Mpro.


Subject(s)
COVID-19 , Pharmaceutical Preparations , Coronavirus 3C Proteases , Drug Repositioning , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protease Inhibitors/pharmacology , SARS-CoV-2
20.
Recent Adv Drug Deliv Formul ; 16(1): 3-15, 2022.
Article in English | MEDLINE | ID: covidwho-1528764

ABSTRACT

INTRODUCTION: Serious COVID-19 respiratory problems start when the virus reaches the alveolar level, where type II cells get infected and die. Therefore, virus inhibition at the alveolar level would help preventing these respiratory complications. METHOD: A literature search was conducted to collect physicochemical properties of small molecule compounds that could be used for the COVID-19 treatment. Compounds with low melting points were selected along with those soluble in ethanol, hydrogen-bond donors, and acceptors. RESULTS: There are severe acute respiratory syndrome coronavirus inhibitors with physicochemical properties suitable for the formulation as an ultrafine pressurised metered-dose inhaler (pMDI). Mycophenolic acid, Debio 025, and cyclosporine A are prime candidates among these compounds. Cyclosporine A (hereafter cyclosporine) is a potent SARS-CoV-2 inhibitor, and it has been used for the treatment of COVID-19 patients, demonstrating an improved survival rate. Also, inhalation therapy of nebulised cyclosporine was tolerated, which was used for patients with lung transplants. Finally, cyclosporine has been formulated as a solution ultrafine pMDI. Although vaccine therapy has started in most countries, inhalation therapies with non-immunological activities could minimise the spread of the disease and be used in vaccine-hesitant individuals. CONCLUSION: Ultrafine pMDI formulation of cyclosporine or Debio 025 should be investigated for the inhalation therapy of COVID-19.


Subject(s)
COVID-19 Drug Treatment , Cyclosporine/therapeutic use , Humans , Nebulizers and Vaporizers , SARS-CoV-2
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