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Chavda V, Dodiya P, Apostolopoulos V. Adverse drug reactions associated with COVID-19 management. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:7353-7376. [PMID: 38743117 DOI: 10.1007/s00210-024-03137-0] [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: 01/09/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
The emergence of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak, which causes COVID-19, had a devastating impact on both people's lives and the global economy. During the course of the pandemic, the lack of specific drugs or treatments tailored for COVID-19 led to extensive repurposing of existing drugs in the pursuit of effective treatments. Some drug molecules demonstrated efficacy, while others proved ineffective. In this context, the approach of drug repurposing emerged as a novel strategy for combating COVID-19. Repurposed drugs and biologics have shown effectiveness, leading to improved clinical outcomes among patients with COVID-19. Similarly, It is equally important to assess the risk-benefit ratio associated with drugs and biologics adapted for COVID-19 treatment. Herein, we primarily focus on evaluating adverse drug events linked to repurposed COVID-19 medications, repurposed biologics, and COVID-specific drug molecules.
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Affiliation(s)
- Vivek Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India.
| | - Payal Dodiya
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia.
- Australian Institute for Musculoskeletal Science, Melbourne, VIC, Australia.
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Alduaij OK, Hussein RK, Abu Alrub S, Zidan SAH. Antimicrobial activities of Diltiazem Hydrochloride: drug repurposing approach. PeerJ 2024; 12:e17809. [PMID: 39329140 PMCID: PMC11426324 DOI: 10.7717/peerj.17809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 09/28/2024] Open
Abstract
Background The growing concern of antibiotic-resistant microbial strains worldwide has prompted the need for alternative methods to combat microbial resistance. Biofilm formation poses a significant challenge to antibiotic efficiency due to the difficulty of penetrating antibiotics through the sticky microbial aggregates. Drug repurposing is an innovative technique that aims to expand the use of non-antibiotic medications to address this issue. The primary objective of this study was to evaluate the antimicrobial properties of Diltiazem HCl, a 1,5-benzothiazepine Ca2 + channel blocker commonly used as an antihypertensive agent, against four pathogenic bacteria and three pathogenic yeasts, as well as its antiviral activity against the Coxsackie B4 virus (CoxB4). Methods To assess the antifungal and antibacterial activities of Diltiazem HCl, the well diffusion method was employed, while crystal violet staining was used to determine the anti-biofilm activity. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) colorimetric assay was utilized to evaluate the antiviral activity of Diltiazem HCl against the CoxB4 virus. Results This study revealed that Diltiazem HCl exhibited noticeable antimicrobial properties against Gram-positive bacteria, demonstrating the highest inhibition of Staphylococcus epidermidis, followed by Staphylococcus aureus. It effectively reduced the formation of biofilms by 95.1% and 90.7% for S. epidermidis, and S. aureus, respectively. Additionally, the antiviral activity of Diltiazem HCl was found to be potent against the CoxB4 virus, with an IC50 of 35.8 ± 0.54 μg mL-1 compared to the reference antiviral Acyclovir (IC50 42.71 ± 0.43 μg mL-1). Conclusion This study suggests that Diltiazem HCl, in addition to its antihypertensive effect, may also be a potential treatment option for infections caused by Gram-positive bacteria and the CoxB4 viruses, providing an additional off-target effect for Diltiazem HCl.
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Affiliation(s)
- Omar K. Alduaij
- Department of Physics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Rageh K. Hussein
- Department of Physics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Sharif Abu Alrub
- Department of Physics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Sabry A. H. Zidan
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut, Egypt
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Monteonofrio L, Virdia I, Pozzi S, Quadri R, Amendolare A, Marzano F, Braile M, Sulfaro V, Paroni M, Tullo A, Soddu S, Guerrini L. Molecular mechanisms of thalidomide effectiveness on COVID-19 patients explained: ACE2 is a new ΔNp63α target gene. J Mol Med (Berl) 2024:10.1007/s00109-024-02485-x. [PMID: 39294414 DOI: 10.1007/s00109-024-02485-x] [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: 03/26/2024] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024]
Abstract
COVID-19 pandemic is caused by the SARS-CoV-2 virus, whose internalization and infection are mediated by the angiotensin-converting enzyme 2 (ACE2). The identification of novel approaches to tackle this step is instrumental for the development of therapies for the management of COVID-19 and other diseases with a similar mechanism of infection. Thalidomide, a drug sadly known for its teratogenic effects, has potent immunomodulatory and anti-inflammatory properties. Treatment with this drug has been shown to improve the immune functions of COVID-19 patients and proposed for the management of COVID-19 in clinical practice through drug repositioning. Here, we investigated the molecular details linking thalidomide to ACE2 and COVID-19, showing that in conditions mimicking SARS-CoV-2-associated cytokine storm, the transcription factor ΔNp63α and ACE2 are stabilized, and IL-8 production is increased. In such conditions, we found p63 to bind to and regulate the expression of the ACE2 gene. We previously showed that ΔNp63α is degraded upon thalidomide treatment and now found that treatment with this drug-or with its analogue lenalidomide-downregulates ACE2 in a p63-dependent manner. Finally, we found that thalidomide treatment reduces in vitro infection by pseudo-SARS-CoV-2, a baculovirus pseudotyped with the SARS-CoV-2 spike protein. Overall, we propose the dual effect of thalidomide in reducing SARS-CoV-2 viral re-entry and inflammation through p63 degradation to weaken SARS-CoV-2 entry into host cells and mitigate lung inflammation, making it a valuable option in clinical management of COVID-19. KEY MESSAGES: Thalidomide treatment results in p63-dependent ACE2 downregulation. ACE2 is a p63 transcriptional target. Thalidomide reduces the "cytokine storm" associated to COVID-19. Thalidomide prevents viral re-entry of SARS-CoV-2 by p63-dependent ACE2 downregulation. Thalidomide is a modulator of SARS-CoV-2 or other ACE2-dependent infections. ACE2 is modulated by a pharmacological substance.
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Affiliation(s)
- Laura Monteonofrio
- Dipartimento Di Ricerca E Tecnologie Avanzate, Istituto Nazionale Tumori Regina Elena IRCCS, 00144, Rome, Italy
| | - Ilaria Virdia
- Dipartimento Di Ricerca E Tecnologie Avanzate, Istituto Nazionale Tumori Regina Elena IRCCS, 00144, Rome, Italy
| | - Sara Pozzi
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Roberto Quadri
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Alessandra Amendolare
- Istituto Di Biomembrane, Bioenergetica E Biotecnologie Molecolari (IBIOM), Consiglio Nazionale Delle Ricerche, 70025, Bari, Italy
| | - Flaviana Marzano
- Istituto Di Biomembrane, Bioenergetica E Biotecnologie Molecolari (IBIOM), Consiglio Nazionale Delle Ricerche, 70025, Bari, Italy
| | - Micaela Braile
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Virginia Sulfaro
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Moira Paroni
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Apollonia Tullo
- Istituto Di Biomembrane, Bioenergetica E Biotecnologie Molecolari (IBIOM), Consiglio Nazionale Delle Ricerche, 70025, Bari, Italy
| | - Silvia Soddu
- Dipartimento Di Ricerca E Tecnologie Avanzate, Istituto Nazionale Tumori Regina Elena IRCCS, 00144, Rome, Italy
| | - Luisa Guerrini
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy.
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Poonia N, Jadhav NV, Mamatha D, Garg M, Kabra A, Bhatia A, Ojha S, Lather V, Pandita D. Nanotechnology-assisted combination drug delivery: a progressive approach for the treatment of acute myeloid leukemia. Ther Deliv 2024:1-18. [PMID: 39268925 DOI: 10.1080/20415990.2024.2394012] [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: 01/11/2024] [Accepted: 08/15/2024] [Indexed: 09/15/2024] Open
Abstract
Acute myeloid leukemia (AML), a heterogeneous hematopoietic cancer prevalent in adults, has been a leading cause of leukemia-associated deaths for decades. Despite advancements in understanding its pathology and pharmacological targets, therapeutic strategies have seen minimal change. The standard treatment, combining cytarabine and anthracycline, has persisted, accompanied by challenges such as pharmacokinetic issues and non-specific drug delivery, leading to severe side effects. Nanotechnology offers a promising solution through combination drug delivery. FDA-approved CPX351 (VYXEOS™) a liposomal formulation delivering doxorubicin and cytarabine, exemplifies enhanced therapeutic efficacy. Ongoing research explores various nanocarriers for delivering multiple bioactives, addressing drug targeting, pharmacokinetics and chemoresistance. This review highlights nanotechnology-based combination therapies for the effective management of AML, presenting a potential breakthrough in leukemia.
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Affiliation(s)
- Neelam Poonia
- University Institute of Pharma Sciences, Chandigarh University, Gharuan, Mohali, Punjab, India
| | - Nikita Vijay Jadhav
- Department of Pharmaceutics, Delhi Institute of Pharmaceutical Sciences & Research (DIPSAR), Delhi Pharmaceutical Sciences & Research University, Pushp Vihar, Govt. of NCT of Delhi, New Delhi, 110017, India
| | - Davuluri Mamatha
- Department of Pharmaceutics, Delhi Institute of Pharmaceutical Sciences & Research (DIPSAR), Delhi Pharmaceutical Sciences & Research University, Pushp Vihar, Govt. of NCT of Delhi, New Delhi, 110017, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector-125, Noida, 201313, India
| | - Atul Kabra
- University Institute of Pharma Sciences, Chandigarh University, Gharuan, Mohali, Punjab, India
| | - Amit Bhatia
- Department of Pharmaceutical Sciences & Technology, Maharaja Ranjit Singh Punjab Technical University (Govt of Punjab), Dabwali Road, Bathinda, Punjab, 151001, India
| | - Shreesh Ojha
- Pharmacology, College of Medicine & Health Sciences, P.O. Box 15551, Al Ain, UAE
| | - Viney Lather
- Amity Institute of Pharmacy, Amity University, Noida, 201313, Uttar Pradesh, India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Institute of Pharmaceutical Sciences & Research (DIPSAR), Delhi Pharmaceutical Sciences & Research University, Pushp Vihar, Govt. of NCT of Delhi, New Delhi, 110017, India
- Centre for Advanced Formulation & Technology (CAFT), Delhi Pharmaceutical Sciences & Research University, Pushp Vihar, Govt. of NCT of Delhi, New Delhi, 110017, India
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Yang D, Ning J, Zhang Y, Xu X, Zhang D, Fan H, Wang J, Lu G. In vitro assessment of the anti-adenoviral activity of artemisinin and its derivatives. Virus Res 2024; 349:199448. [PMID: 39127240 PMCID: PMC11403056 DOI: 10.1016/j.virusres.2024.199448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/04/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Adenoviral infections, particularly in children, remain a significant public health issue with no approved targeted treatments. Artemisinin and its derivatives, well-known for their use in malaria treatment, have shown antiviral activities in recent studies. However, their efficacy against human adenovirus (HAdV) remains unexplored. This study aimed to assess the activity of artemisinin and its derivatives against HAdV infection in vitro using cell lines and primary cells. Our data revealed that artemisinin exhibited dose-dependent anti-HAdV activity with no apparent cytotoxicity over a wide concentration range. Mechanistically, artemisinin did not affect viral attachment or entry into target cells, nor the viral genome entry into cell nucleus. Instead, it inhibited HAdV through suppression of viral DNA replication. Comparative analysis with its derivatives, artesunate and artemisone, showed distinct cytotoxicity and anti-adenoviral profiles, with artemisone showing superior efficacy and lower toxicity. Further validation using a primary airway epithelial cell model confirmed the anti-adenoviral activity of both artemisinin and artemisone against different virus strains. Together, our findings suggest that artemisinin and its derivatives may be promising candidates for anti-HAdV treatment.
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Affiliation(s)
- Diyuan Yang
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, China; Department of Pediatric Respiratory, Guangzhou women and children's medical center liuzhou hospital, Guangxi, Liuzhou, 545006, China
| | - Jing Ning
- Department of Children's Health Care, Guangdong Women and Children Hospital, Guangzhou Medical University, Guangzhou, 511442, China
| | - Yuyu Zhang
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Xuehua Xu
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Dongwei Zhang
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Huifeng Fan
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, China
| | - Jing Wang
- Department of Children's Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Gen Lu
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, China.
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Olalekan SO, Obakachi VA, Badeji AA, Akinsipo (Oyelaja) OB, Familoni O, Asekun OT, Oladipo SD, Osinubi AD. Exploring the therapeutic potential of prolinamides as multi-targeted agents for Alzheimer's disease treatment: molecular docking and molecular dynamic simulation studies. In Silico Pharmacol 2024; 12:80. [PMID: 39224128 PMCID: PMC11365881 DOI: 10.1007/s40203-024-00250-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
Alzheimer's disease (AD) presents a significant global health challenge, with its prevalence expected to rise sharply in the coming years. Despite extensive research, effective treatments addressing the multifaceted pathophysiology of AD remain elusive. This study investigates the therapeutic potential of twenty-seven prolinamides (P1 - P27), with the focus on their interactions with key proteins implicated in AD pathogenesis. Four of the compounds, namely; 10-((4-nitrophenyl)prolyl)-10 H-phenothiazine (P14), 2-((4-nitrophenyl)prolyl)isoindoline (P19), 1-(4-formylphenyl)-N-(p-tolyl)pyrrolidine-2-carboxamide (P22), and N,1-bis(4-nitrophenyl)pyrrolidine-2-carboxamide (P27) showed promising potential as Alzheimer's drug. In-silico approaches including molecular docking, molecular dynamic (MD) simulation, post md study, physicochemical and drug-likeness parameters were employed to ascertain the potential of these compounds as inhibitors of certain proteins implicated in the pathophysiology of Alzheimer's disease. Molecular docking and dynamics simulations demonstrated that P14, P19, P22 and P27 exhibited promising binding affinities towards crucial AD-associated proteins, including Beta-Secretase 1 (BACE1), Butyrylcholinesterase (BuChE), and Tau-tubulin kinase 2 (TTBK2). Structural stability analyses revealed that prolinamides, particularly P22 and P27 for BACE1 and P14 and P19 for BuChE, exhibited greater stability than their reference ligands, indicated by lower RMSD, RoG, and RMSF values. For BuChE, Rivastigmine had a docking score of -7.0 kcal/mol, a binding free energy (ΔGbind) of -22.19 ± 2.44 kcal/mol, RMSD of 1.361 ± 0.162 Å, RMSF of 9.357 ± 3.212 Å, and RoG of 22.919 ± 0.064 Å, whereas P19 exhibited a superior docking score of -10.3 kcal/mol, a significantly better ΔGbind of -33.74 ± 2.84 kcal/mol, RMSD of 1.347 ± 0.132 Å, RMSF of 8.164 ± 2.748 Å, and RoG of 22.868 ± 0.070 Å. Physicochemical and pharmacokinetic assessments affirmed the drug-likeness and bioavailability of P19 notably capable of penetrating the blood-brain barrier. Compounds P19 and P22, emerged as multi-targeted ligands, offering the potential for simultaneous modulation of multiple AD-related pathways. These findings highlight the possibilities of these compounds to be explored as novel therapeutic agents for AD. They also highlight the need for further experimental validation to confirm their efficacy and safety profiles, advancing them toward clinical application in AD management. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00250-z.
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Affiliation(s)
- Samuel O. Olalekan
- Department of Physiology, Olabisi Onabanjo University, Sagamu Campus, Sagamu, Ogun State Nigeria
| | - Vincent A. Obakachi
- Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028 South Africa
| | - Abosede A. Badeji
- Department of Chemical Sciences, Tai Solarin University of Education, Ijagun, P.M.B. 2118, Ijebu Ode, Ogun State Nigeria
| | | | - Oluwole Familoni
- Drug Design Research Group, Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, 101245 Nigeria
| | - Olayinka T. Asekun
- Drug Design Research Group, Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, 101245 Nigeria
| | - Segun D. Oladipo
- Department of Chemistry and Polymer Science, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
- Department of Chemical Sciences, Olabisi Onabanjo University, P.M.B 2002, Ago-Iwoye, Nigeria
| | - Adejoke D. Osinubi
- Department of Chemical Sciences, Tai Solarin University of Education, Ijagun, P.M.B. 2118, Ijebu Ode, Ogun State Nigeria
- Drug Design Research Group, Department of Chemistry, University of Lagos, Akoka-Yaba, Lagos, 101245 Nigeria
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Zheng X, He Y, Xia B, Tang W, Zhang C, Wang D, Tang H, Zhao P, Peng H, Liu Y. Etravirine Prevents West Nile Virus and Chikungunya Virus Infection Both In Vitro and In Vivo by Inhibiting Viral Replication. Pharmaceutics 2024; 16:1111. [PMID: 39339151 PMCID: PMC11435157 DOI: 10.3390/pharmaceutics16091111] [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: 07/16/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024] Open
Abstract
Diseases transmitted by arthropod-borne viruses such as West Nile virus (WNV) and chikungunya virus (CHIKV) pose threat to global public health. Unfortunately, to date, there is no available approved drug for severe symptoms caused by both viruses. It has been reported that reverse transcriptase inhibitors can effectively inhibit RNA polymerase activity of RNA viruses. We screened the anti-WNV activity of the FDA-approved reverse transcriptase inhibitor library and found that 4 out of 27 compounds showed significant antiviral activity. Among the candidates, etravirine markedly inhibited WNV infection in both Huh 7 and SH-SY5Y cells. Further assays revealed that etravirine inhibited the infection of multiple arboviruses, including yellow fever virus (YFV), tick-borne encephalitis virus (TBEV), and CHIKV. A deeper study at the phase of action showed that the drug works primarily during the viral replication process. This was supported by the strong interaction potential between etravirine and the RNA-dependent RNA polymerase (RdRp) of WNV and alphaviruses, as evaluated using molecular docking. In vivo, etravirine significantly rescued mice from WNV infection-induced weight loss, severe neurological symptoms, and death, as well as reduced the viral load and inflammatory cytokines in target tissues. Etravirine showed antiviral effects in both arthrophlogosis and lethal mouse models of CHIKV infection. This study revealed that etravirine is an effective anti-WNV and CHIKV arbovirus agent both in vitro and in vivo due to the inhibition of viral replication, providing promising candidates for clinical application.
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Affiliation(s)
- Xu Zheng
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Yanhua He
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Binghui Xia
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Wanda Tang
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Congcong Zhang
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Dawei Wang
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Hailin Tang
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Ping Zhao
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Haoran Peng
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
| | - Yangang Liu
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai 200433, China; (X.Z.); (Y.H.); (B.X.); (W.T.); (C.Z.); (D.W.); (H.T.); (P.Z.)
- Key Laboratory of Biological Defense, Ministry of Education, Naval Medical University, Shanghai 200433, China
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8
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Shafiq N, Jannat A, Munir H, Rashid M, Parveen S. Exploring the potential of FDA approved anti-diabetic drugs for repurposing against COVID-19: a core combination of multiple computational strategies and integrated artificial intelligence. J Biomol Struct Dyn 2024; 42:6556-6576. [PMID: 37455488 DOI: 10.1080/07391102.2023.2234993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
The latest variant of coronavirus is omicron. The World Health Organization (WHO) designated variation 'B.1.1.529' named omicron as a variant of concern (VOC) on 26 November 2021. By September 2020, it will have infected over 16 million patients and killed over 600,000 people over the world. This very infectious viral illness still poses a danger to world health; it has also become the greatest problem the world is facing and become the main area of research. The development of vaccines is insufficient to stop their spread and serious effects. Despite several reputable pharmaceutical firms claiming to have developed a cure for COVID-19. For that purpose, the field-based 3D-QSAR model has been used to analyze a series of anti-diabetic drugs to repurpose them against COVID-19. The LOO verified partial least square (PLS) model generates satisfactory q2 (0.4) and r2 (0.5) values. By using this model 10 compounds were screened out of 55 FDA approved anti-diabetic drugs (built-up library). Additionally, these substances were examined using molecular docking screening and ADMET. Finally, the drugs L8, and L23 were discovered to be the lead drugs. Density functional theory at the B3LYP/6-311G* technique was used to examine structural geometries, electronic characteristics, and molecular electrostatic potential (MEP). This work will greatly assist in the detection and development of leads for early drug development to control COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Aqsa Jannat
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Huma Munir
- Green Chemistry Lab., Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
- Department of Applied Chemistry, Beijing Institute of Technology, Beijing, China
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D'Souza SE, Khan K, Jalal K, Hassam M, Uddin R. The Gene Network Correlation Analysis of Obesity to Type 1 Diabetes and Cardiovascular Disorders: An Interactome-Based Bioinformatics Approach. Mol Biotechnol 2024; 66:2123-2143. [PMID: 37606877 DOI: 10.1007/s12033-023-00845-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/29/2023] [Indexed: 08/23/2023]
Abstract
The current study focuses on the importance of Protein-Protein Interactions (PPIs) in biological processes and the potential of targeting PPIs as a new treatment strategy for diseases. Specifically, the study explores the cross-links of PPIs network associated with obesity, type 1 diabetes mellitus (T1DM), and cardiac disease (CD), which is an unexplored area of research. The research aimed to understand the role of highly connected proteins in the network and their potential as drug targets. The methodology for this research involves retrieving genes from the NCBI online gene database, intersecting genes among three diseases (type 1 diabetes, obesity, and cardiovascular) using Interactivenn, determining suitable drug molecules using NetworkAnalyst, and performing various bioinformatics analyses such as Generic Protein-Protein Interactions, topological properties analysis, function enrichment analysis in terms of GO, and Kyoto Encyclopedia of Genes and Genomes (KEGG), gene co-expression network, and protein drug as well as protein chemical interaction network. The study focuses on human subjects. The results of this study identified 12 genes [VEGFA (Vascular Endothelial Growth Factor A), IL6 (Interleukin 6), MTHFR (Methylenetetrahydrofolate reductase), NPPB (Natriuretic Peptide B), RAC1 (Rac Family Small GTPase 1), LMNA (Lamin A/C), UGT1A1 (UDP-glucuronosyltransferase family 1 membrane A1), RETN (Resistin), GCG (Glucagon), NPPA (Natriuretic Peptide A), RYR2 (Ryanodine receptor 2), and PRKAG2 (Protein Kinase AMP-Activated Non-Catalytic Subunit Gamma 2)] that were shared across the three diseases and could be used as key proteins for protein-drug/chemical interaction. Additionally, the study provides an in-depth understanding of the complex molecular and biological relationships between the three diseases and the cellular mechanisms that lead to their development. Potentially significant implications for the therapy and management of various disorders are highlighted by the findings of this study by improving treatment efficacy, simplifying treatment regimens, cost-effectiveness, better understanding of the underlying mechanism of these diseases, early diagnosis, and introducing personalized medicine. In conclusion, the current study provides new insights into the cross-links of PPIs network associated with obesity, T1DM, and CD, and highlights the potential of targeting PPIs as a new treatment strategy for these prevalent diseases.
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Affiliation(s)
- Sharon Elaine D'Souza
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Lab 103 PCMD Ext., Karachi, 75270, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Lab 103 PCMD Ext., Karachi, 75270, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Hassam
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Lab 103 PCMD Ext., Karachi, 75270, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Lab 103 PCMD Ext., Karachi, 75270, Pakistan.
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10
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Abisheva S, Rutskaya-Moroshan K, Nuranova G, Batyrkhan T, Abisheva A. Antimalarial Drugs at the Intersection of SARS-CoV-2 and Rheumatic Diseases: What Are the Potential Opportunities? MEDICINA (KAUNAS, LITHUANIA) 2024; 60:1171. [PMID: 39064600 PMCID: PMC11279047 DOI: 10.3390/medicina60071171] [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: 05/29/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Background and Objectives: The coronavirus disease of 2019 (COVID-19) pandemic has posed a serious threat to humanity and is considered a global health emergency. Antimalarial drugs (ADs) have been used in the treatment of immuno-inflammatory arthritis (IIA) and coronavirus infection (COVID-19). The aim of this review is to analyze the current knowledge about the immunomodulatory and antiviral mechanisms of action, characteristics of use, and side effects of antimalarial drugs. Material and Methods: A literature search was carried out using PubMed, MEDLINE, SCOPUS, and Google Scholar databases. The inclusion criteria were the results of randomized and cohort studies, meta-analyses, systematic reviews, and original full-text manuscripts in the English language containing statistically confirmed conclusions. The exclusion criteria were summary reports, newspaper articles, and personal messages. Qualitative methods were used for theoretical knowledge on antimalarial drug usage in AIRDs and SARS-CoV-2 such as a summarization of the literature and a comparison of the treatment methods. Results: The ADs were considered a "candidate" for the therapy of a new coronavirus infection due to mechanisms of antiviral activity, such as interactions with endocytic pathways, the prevention of glycosylation of the ACE2 receptors, blocking sialic acid receptors, and reducing the manifestations of cytokine storms. The majority of clinical trials suggest no role of antimalarial drugs in COVID-19 treatment or prevention. These circumstances do not allow for their use in the treatment and prevention of COVID-19. Conclusions: The mechanisms of hydroxychloroquine are related to potential cardiotoxic manifestations and demonstrate potential adverse effects when used for COVID-19. Furthermore, the need for high doses in the treatment of viral infections increases the likelihood of gastrointestinal side effects, the prolongation of QT, and retinopathy. Large randomized clinical trials (RCTs) have refuted the fact that there is a positive effect on the course and results of COVID-19.
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Affiliation(s)
- Saule Abisheva
- Department of Family Medicine №1, NJSC “Astana Medical University”, Astana 010000, Kazakhstan; (S.A.); (T.B.); (A.A.)
| | - Kristina Rutskaya-Moroshan
- Department of Family Medicine №1, NJSC “Astana Medical University”, Astana 010000, Kazakhstan; (S.A.); (T.B.); (A.A.)
| | - Gulnaz Nuranova
- Department of Children’s Diseases with Courses in Pulmonology and Nephrology, NJSC “Astana Medical University”, Astana 010000, Kazakhstan;
| | - Tansholpan Batyrkhan
- Department of Family Medicine №1, NJSC “Astana Medical University”, Astana 010000, Kazakhstan; (S.A.); (T.B.); (A.A.)
| | - Anilim Abisheva
- Department of Family Medicine №1, NJSC “Astana Medical University”, Astana 010000, Kazakhstan; (S.A.); (T.B.); (A.A.)
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11
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Kombo DC, Stepp JD, Lim S, Elshorst B, Li Y, Cato L, Shomali M, Fink D, LaMarche MJ. Predictions of Colloidal Molecular Aggregation Using AI/ML Models. ACS OMEGA 2024; 9:28691-28706. [PMID: 38973835 PMCID: PMC11223200 DOI: 10.1021/acsomega.4c02886] [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: 03/28/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024]
Abstract
To facilitate the triage of hits from small molecule screens, we have used various AI/ML techniques and experimentally observed data sets to build models aimed at predicting colloidal aggregation of small organic molecules in aqueous solution. We have found that Naïve Bayesian and deep neural networks outperform logistic regression, recursive partitioning tree, support vector machine, and random forest techniques by having the lowest balanced error rate (BER) for the test set. Derived predictive classification models consistently and successfully discriminated aggregator molecules from nonaggregator hits. An analysis of molecular descriptors in favor of colloidal aggregation confirms previous observations (hydrophobicity, molecular weight, and solubility) in addition to undescribed molecular descriptors such as the fraction of sp3 carbon atoms (Fsp3), and electrotopological state of hydroxyl groups (ES_Sum_sOH). Naïve Bayesian modeling and scaffold tree analysis have revealed chemical features/scaffolds contributing the most to colloidal aggregation and nonaggregation, respectively. These results highlight the importance of scaffolds with high Fsp3 values in promoting nonaggregation. Matched molecular pair analysis (MMPA) has also deciphered context-dependent substitutions, which can be used to design nonaggregator molecules. We found that most matched molecular pairs have a neutral effect on aggregation propensity. We have prospectively applied our predictive models to assist in chemical library triage for optimal plate selection diversity and purchase for high throughput screening (HTS) in drug discovery projects.
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Affiliation(s)
- David C. Kombo
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - J. David Stepp
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Sungtaek Lim
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Bettina Elshorst
- CMC
Synthetics Early Development Analytics, Sanofi, Industriepark Hochst, Frankfurt 65926, Germany
| | - Yi Li
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Laura Cato
- Molecular
Oncology, Sanofi, 350
Water St., Cambridge, Massachusetts 02141, United States
| | - Maysoun Shomali
- Molecular
Oncology, Sanofi, 350
Water St., Cambridge, Massachusetts 02141, United States
| | - David Fink
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
| | - Matthew J. LaMarche
- Integrated
Drug Discovery, Sanofi, 350 Water St., Cambridge, Massachusetts 02141, United States
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12
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Hershan AA. Pathogenesis of COVID19 and the applications of US FDA-approved repurposed antiviral drugs to combat SARS-CoV-2 in Saudi Arabia: A recent update by review of literature. Saudi J Biol Sci 2024; 31:104023. [PMID: 38799719 PMCID: PMC11127266 DOI: 10.1016/j.sjbs.2024.104023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Still, there is no cure for the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused coronavirus disease 2019 (COVID19). The COVID19 pandemic caused health emergencies which resulted in enormous medical and financial consequences worldwide including Saudi Arabia. Saudi Arabia is the largest Arab country of the Middle East. The urban setting of Saudi Arabia makes it vulnerable towards SARS-CoV-2 (SCV-2). Religious areas of this country are visited by millions of pilgrims every year for the Umrah and Hajj pilgrimage, which contributes to the potential COVID19 epidemic risk. COVID19 throws various challenges to healthcare professionals to choose the right drugs or therapy in clinical settings because of the lack of availability of newer drugs. Current drug development and discovery is an expensive, complex, and long process, which involves a high failure rate in clinical trials. While repurposing of United States Food and Drug Administration (US FDA)-approved antiviral drugs offers numerous benefits including complete pharmacokinetic and safety profiles, which significantly shorten drug development cycles and reduce costs. A range of repurposed US FDA-approved antiviral drugs including ribavirin, lopinavir/ritonavir combination, oseltamivir, darunavir, remdesivir, nirmatrelvir/ritonavir combination, and molnupiravir showed encouraging results in clinical trials in COVID19 treatment. In this article, several COVID19-related discussions have been provided including emerging variants of concern of, COVID19 pathogenesis, COVID19 pandemic scenario in Saudi Arabia, drug repurposing strategies against SCV-2, as well as repurposing of US FDA-approved antiviral drugs that might be considered to combat SCV-2 in Saudi Arabia. Moreover, drug repurposing in the context of COVID19 management along with its limitations and future perspectives have been summarized.
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Affiliation(s)
- Almonther Abdullah Hershan
- The University of Jeddah, College of Medicine, Department of Medical microbiology and parasitology, Jeddah, Saudi Arabia
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13
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Gharizadeh A, Abbasi K, Ghareyazi A, Mofrad MRK, Rabiee HR. HGTDR: Advancing drug repurposing with heterogeneous graph transformers. Bioinformatics 2024; 40:btae349. [PMID: 38913860 PMCID: PMC11223801 DOI: 10.1093/bioinformatics/btae349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 04/20/2024] [Accepted: 06/23/2024] [Indexed: 06/26/2024] Open
Abstract
MOTIVATION Drug repurposing is a viable solution for reducing the time and cost associated with drug development. However, thus far, the proposed drug repurposing approaches still need to meet expectations. Therefore, it is crucial to offer a systematic approach for drug repurposing to achieve cost savings and enhance human lives. In recent years, using biological network-based methods for drug repurposing has generated promising results. Nevertheless, these methods have limitations. Primarily, the scope of these methods is generally limited concerning the size and variety of data they can effectively handle. Another issue arises from the treatment of heterogeneous data, which needs to be addressed or converted into homogeneous data, leading to a loss of information. A significant drawback is that most of these approaches lack end-to-end functionality, necessitating manual implementation and expert knowledge in certain stages. RESULTS We propose a new solution, Heterogeneous Graph Transformer for Drug Repurposing (HGTDR), to address the challenges associated with drug repurposing. HGTDR is a three-step approach for knowledge graph-based drug repurposing: (1) constructing a heterogeneous knowledge graph, (2) utilizing a heterogeneous graph transformer network, and (3) computing relationship scores using a fully connected network. By leveraging HGTDR, users gain the ability to manipulate input graphs, extract information from diverse entities, and obtain their desired output. In the evaluation step, we demonstrate that HGTDR performs comparably to previous methods. Furthermore, we review medical studies to validate our method's top 10 drug repurposing suggestions, which have exhibited promising results. We also demonstrated HGTDR's capability to predict other types of relations through numerical and experimental validation, such as drug-protein and disease-protein inter-relations. AVAILABILITY AND IMPLEMENTATION The source code and data are available at https://github.com/bcb-sut/HGTDR and http://git.dml.ir/BCB/HGTDR.
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Affiliation(s)
- Ali Gharizadeh
- Department of Computer Engineering, Sharif University of Technology, Tehran, P.O. Box 11155-9517, Iran
| | - Karim Abbasi
- Department of Computer Engineering, Sharif University of Technology, Tehran, P.O. Box 11155-9517, Iran
| | - Amin Ghareyazi
- Department of Computer Engineering, Sharif University of Technology, Tehran, P.O. Box 11155-9517, Iran
| | - Mohammad R K Mofrad
- Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, P.O. Box 94720-1740, United States
| | - Hamid R Rabiee
- Department of Computer Engineering, Sharif University of Technology, Tehran, P.O. Box 11155-9517, Iran
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14
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Ma MT, Jiang Q, Chen CH, Badeti S, Wang X, Zeng C, Evans D, Bodnar B, Marras SAE, Tyagi S, Bharaj P, Yehia G, Romanienko P, Hu W, Liu SL, Shi L, Liu D. S309-CAR-NK cells bind the Omicron variants in vitro and reduce SARS-CoV-2 viral loads in humanized ACE2-NSG mice. J Virol 2024; 98:e0003824. [PMID: 38767356 PMCID: PMC11237809 DOI: 10.1128/jvi.00038-24] [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: 01/29/2024] [Accepted: 04/11/2024] [Indexed: 05/22/2024] Open
Abstract
Recent progress on chimeric antigen receptor (CAR)-NK cells has shown promising results in treating CD19-positive lymphoid tumors with minimal toxicities [including graft versus host disease (GvHD) and cytokine release syndrome (CRS) in clinical trials. Nevertheless, the use of CAR-NK cells in combating viral infections has not yet been fully explored. Previous studies have shown that CAR-NK cells expressing S309 single-chain fragment variable (scFv), hereinafter S309-CAR-NK cells, can bind to SARS-CoV-2 wildtype pseudotyped virus (PV) and effectively kill cells expressing wild-type spike protein in vitro. In this study, we further demonstrate that the S309-CAR-NK cells can bind to different SARS-CoV-2 variants, including the B.1.617.2 (Delta), B.1.621 (Mu), and B.1.1.529 (Omicron) variants in vitro. We also show that S309-CAR-NK cells reduce virus loads in the NOD/SCID gamma (NSG) mice expressing the human angiotensin-converting enzyme 2 (hACE2) receptor challenged with SARS-CoV-2 wild-type (strain USA/WA1/2020). Our study demonstrates the potential use of S309-CAR-NK cells for inhibiting infection by SARS-CoV-2 and for the potential treatment of COVID-19 patients unresponsive to otherwise currently available therapeutics. IMPORTANCE Chimeric antigen receptor (CAR)-NK cells can be "off-the-shelf" products that treat various diseases, including cancer, infections, and autoimmune diseases. In this study, we engineered natural killer (NK) cells to express S309 single-chain fragment variable (scFv), to target the Spike protein of SARS-CoV-2, hereinafter S309-CAR-NK cells. Our study shows that S309-CAR-NK cells are effective against different SARS-CoV-2 variants, including the B.1.617.2 (Delta), B.1.621 (Mu), and B.1.1.529 (Omicron) variants. The S309-CAR-NK cells can (i) directly bind to SARS-CoV-2 pseudotyped virus (PV), (ii) competitively bind to SARS-CoV-2 PV with 293T cells expressing the human angiotensin-converting enzyme 2 (hACE2) receptor (293T-hACE2 cells), (iii) specifically target and lyse A549 cells expressing the spike protein, and (iv) significantly reduce the viral loads of SARS-CoV-2 wild-type (strain USA/WA1/2020) in the lungs of NOD/SCID gamma (NSG) mice expressing hACE2 (hACE2-NSG mice). Altogether, the current study demonstrates the potential use of S309-CAR-NK immunotherapy as an alternative treatment for COVID-19 patients.
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Affiliation(s)
- Minh Tuyet Ma
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Qingkui Jiang
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Chih-Hsiung Chen
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Saiaditya Badeti
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Xuening Wang
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
| | - Cong Zeng
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
| | - Deborah Evans
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Brittany Bodnar
- Center for Metabolic Disease Research, Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Salvatore A. E. Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Preeti Bharaj
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Ghassan Yehia
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Peter Romanienko
- Genome Editing Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
| | - Lanbo Shi
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Dongfang Liu
- Department of Pathology, Immunology, and Laboratory Medicine, South Orange Avenue, Newark, New Jersey, USA
- School of Graduate Studies, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, USA
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15
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Rohweder R, Pereira NG, Micheletti BH, Mosello J, Campos JRM, Pereira MG, Santos CN, Simões NL, Matielo RLB, Bernardes LS, Oppermann MLR, Wender MCO, Lupattelli A, Nordeng H, Schuler-Faccini L. Medication Use Among Pregnant Women With SARS-CoV-2 Infection and Risk of Hospitalization-A Study in Two Brazilian Hospitals. J Pregnancy 2024; 2024:8915166. [PMID: 39021875 PMCID: PMC11254464 DOI: 10.1155/2024/8915166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 07/20/2024] Open
Abstract
There is limited evidence about the use of medications among pregnant women with COVID-19, as well as risk factors for hospitalization due to COVID-19 in pregnancy. We aimed to describe the use of medications among SARS-CoV-2-positive pregnant women at the time around infection and identify predictors for hospitalization due to COVID-19 in two hospitals in Brazil. This is a hospital record-based study among pregnant women with positive SARS-CoV-2 tests between March 2020 and August 2022 from two Brazilian hospitals. Characteristics of sociodemographic, obstetrical, and COVID-19 symptoms were extracted retrospectively. The prevalence use of medications was based on self-reported use, and this was administered at the hospital. Logistic regression was used to estimate predictors of hospitalization due to COVID-19. There were 278 pregnant women included in the study, of which 41 (14.7%) required hospitalization due to COVID-19. The remaining 237 (85.3%) had mild symptoms or were asymptomatic. Most of the women had the infection in the third trimester (n = 149; 53.6%). The most prevalent medications used across all trimesters were analgesics (2.4% to 20.0%), antibacterials (15.0% to 23.1%), and corticosteroids (7.2% to 10.4%). Pre- or gestational hypertensive disorder (odds ratio (OR) 4.94, 95% confidence interval (CI) 1.65, 14.87) and having at least one dose of vaccine against SARS-CoV-2 (OR 0.13, 95% CI 0.04, 0.39) were associated with hospitalization due to COVID-19. Analgesics, antibacterials, and corticosteroids were the most frequently used medications among pregnant women with COVID-19. Women with hypertensive disorders have almost a five-fold increased risk of hospitalization due to COVID-19. Vaccination was the strongest protective factor for severe COVID-19. The COVID-19 vaccination among pregnant women should be promoted, and pregnant women diagnosed with COVID-19 who have hypertensive disorders should be closely monitored.
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Affiliation(s)
- Ricardo Rohweder
- Graduate Program in Genetics and Molecular BiologyDepartment of GeneticsUniversidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Natálya G. Pereira
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Bruna H. Micheletti
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Jéssica Mosello
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Júlia R. M. Campos
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Matheus G. Pereira
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Cristina N. Santos
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Natália L. Simões
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Regina L. B. Matielo
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
| | - Lisandra S. Bernardes
- Department of Obstetrics and NeonatologyHospital e Maternidade SEPACO, São Paulo, Brazil
- Center for Klinisk Forskning and Afdeling for Kvindesygdomme, Graviditet og FødselNorth Denmark Regional Hospital, Hjørring, Denmark
| | - Maria L. R. Oppermann
- Gynecology and Obstetrics ServiceHospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Maria C. O. Wender
- Gynecology and Obstetrics ServiceHospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Angela Lupattelli
- PharmacoEpidemiology and Drug Safety Research GroupDepartment of PharmacyUniversity of Oslo, Oslo, Norway
| | - Hedvig Nordeng
- PharmacoEpidemiology and Drug Safety Research GroupDepartment of PharmacyUniversity of Oslo, Oslo, Norway
| | - Lavinia Schuler-Faccini
- Graduate Program in Genetics and Molecular BiologyDepartment of GeneticsUniversidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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16
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Mizuno Y, Nakasone W, Nakamura M, Otaki JM. In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development. Vaccines (Basel) 2024; 12:539. [PMID: 38793790 PMCID: PMC11125730 DOI: 10.3390/vaccines12050539] [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: 04/30/2024] [Revised: 05/12/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Spike protein sequences in SARS-CoV-2 have been employed for vaccine epitopes, but many short constituent sequences (SCSs) in the spike protein are present in the human proteome, suggesting that some anti-spike antibodies induced by infection or vaccination may be autoantibodies against human proteins. To evaluate this possibility of "molecular mimicry" in silico and in vitro, we exhaustively identified common SCSs (cSCSs) found both in spike and human proteins bioinformatically. The commonality of SCSs between the two systems seemed to be coincidental, and only some cSCSs were likely to be relevant to potential self-epitopes based on three-dimensional information. Among three antibodies raised against cSCS-containing spike peptides, only the antibody against EPLDVL showed high affinity for the spike protein and reacted with an EPLDVL-containing peptide from the human unc-80 homolog protein. Western blot analysis revealed that this antibody also reacted with several human proteins expressed mainly in the small intestine, ovary, and stomach. Taken together, these results showed that most cSCSs are likely incapable of inducing autoantibodies but that at least EPLDVL functions as a self-epitope, suggesting a serious possibility of infection-induced or vaccine-induced autoantibodies in humans. High-risk cSCSs, including EPLDVL, should be excluded from vaccine epitopes to prevent potential autoimmune disorders.
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Affiliation(s)
- Yuya Mizuno
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Wataru Nakasone
- Computer Science and Intelligent Systems Unit, Department of Engineering, Faculty of Engineering, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Morikazu Nakamura
- Computer Science and Intelligent Systems Unit, Department of Engineering, Faculty of Engineering, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
| | - Joji M. Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara 903-0213, Okinawa, Japan
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Mekonen ZT, Fenta TG, Nadeem SP, Cho DJ. Global Health Commodities Supply Chain in the Era of COVID-19 Pandemic: Challenges, Impacts, and Prospects: A Systematic Review. J Multidiscip Healthc 2024; 17:1523-1539. [PMID: 38623396 PMCID: PMC11018129 DOI: 10.2147/jmdh.s448654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Background The COVID-19 pandemic led to the most substantial health crisis in the 21st Century. This pandemic interrupted the supply of essential commodities for human beings. Among the essential commodities for human survival, disruption of the supply of essential health commodities has become a global concern. Objective The study aimed to systematically analyze published articles on the challenges, impacts, and prospects of the global health commodities' supply chain in the era of the COVID-19 pandemic. Methods A standard searching strategy was conducted in seven research databases to retrieve pertinent articles. Finally, 459 articles were retrieved for further screening, and only 13 articles were selected for final synthesis. Results Almost 38.5% of the studies targeted the supply chain of health commodities used to treat HIV, TB, and malaria. Lockdown policies, travel restrictions, lack of transportation, low manufacturing capacity, and rising costs were the significant challenges indicated for the supply interruption of essential health commodities and COVID-19 vaccines. Findings indicated that the supply interruption of essential health commodities leads to a devastating impact on global health. Conclusion Global medicine shortages due to the pandemic crisis can have a devastatingly harmful impact on patient outcomes and might result in a devastatingly long-lasting effect on the health of the world community. Supply-related challenges of the COVID-19 vaccine affect countries' ambitions for achieving herd immunity quickly. Monitoring the pandemic's effect on the health commodities' supply system and designing a short-term and long-term resilient health supply chain system that can cope with current and future health catastrophes is pivotal.
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Affiliation(s)
- Zelalem Tilahun Mekonen
- Department of Pharmaceutics and Social Pharmacy, School of Pharmacy, Addis Ababa University, Addis Ababa, Ethiopia
| | - Teferi Gedif Fenta
- Department of Pharmaceutics and Social Pharmacy, School of Pharmacy, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Denny J Cho
- Logistics Department, Kyrgyz State Technical University, Bishkek, Kyrgyzstan
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18
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Rani N, Kaushik A, Kardam S, Kag S, Raj VS, Ambasta RK, Kumar P. Reimagining old drugs with new tricks: Mechanisms, strategies and notable success stories in drug repurposing for neurological diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:23-70. [PMID: 38789181 DOI: 10.1016/bs.pmbts.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Recent evolution in drug repurposing has brought new anticipation, especially in the conflict against neurodegenerative diseases (NDDs). The traditional approach to developing novel drugs for these complex disorders is laborious, time-consuming, and often abortive. However, drug reprofiling which is the implementation of illuminating novel therapeutic applications of existing approved drugs, has shown potential as a promising strategy to accelerate the hunt for therapeutics. The advancement of computational approaches and artificial intelligence has expedited drug repurposing. These progressive technologies have enabled scientists to analyse extensive datasets and predict potential drug-disease interactions. By prospecting into the existing pharmacological knowledge, scientists can recognise potential therapeutic candidates for reprofiling, saving precious time and resources. Preclinical models have also played a pivotal role in this field, confirming the effectiveness and mechanisms of action of repurposed drugs. Several studies have occurred in recent years, including the discovery of available drugs that demonstrate significant protective effects in NDDs, relieve debilitating symptoms, or slow down the progression of the disease. These findings highlight the potential of repurposed drugs to change the landscape of NDD treatment. Here, we present an overview of recent developments and major advances in drug repurposing intending to provide an in-depth analysis of traditional drug discovery and the strategies, approaches and technologies that have contributed to drug repositioning. In addition, this chapter attempts to highlight successful case studies of drug repositioning in various therapeutic areas related to NDDs and explore the clinical trials, challenges and limitations faced by researchers in the field. Finally, the importance of drug repositioning in drug discovery and development and its potential to address discontented medical needs is also highlighted.
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Affiliation(s)
- Neetu Rani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Shefali Kardam
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Sonika Kag
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India
| | - V Samuel Raj
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University, Delhi, India.
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19
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Sertbas M, Ulgen KO. Uncovering the Effect of SARS-CoV-2 on Liver Metabolism via Genome-Scale Metabolic Modeling for Reprogramming and Therapeutic Strategies. ACS OMEGA 2024; 9:15535-15546. [PMID: 38585079 PMCID: PMC10993323 DOI: 10.1021/acsomega.4c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 04/09/2024]
Abstract
Genome-scale metabolic models (GEMs) are promising computational tools that contribute to elucidating host-virus interactions at the system level and developing therapeutic strategies against viral infection. In this study, the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on liver metabolism was investigated using integrated GEMs of human hepatocytes and SARS-CoV-2. They were generated for uninfected and infected hepatocytes using transcriptome data. Reporter metabolite analysis resulted in significant transcriptional changes around several metabolites involved in xenobiotics, drugs, arachidonic acid, and leukotriene metabolisms due to SARS-CoV-2 infection. Flux balance analysis and minimization of metabolic adjustment approaches unraveled possible virus-induced hepatocellular reprogramming in fatty acid, glycerophospholipid, sphingolipid cholesterol, and folate metabolisms, bile acid biosynthesis, and carnitine shuttle among others. Reaction knockout analysis provided critical reactions in glycolysis, oxidative phosphorylation, purine metabolism, and reactive oxygen species detoxification subsystems. Computational analysis also showed that administration of dopamine, glucosamine, D-xylose, cysteine, and (R)-3-hydroxybutanoate contributes to alleviating viral infection. In essence, the reconstructed host-virus GEM helps us understand metabolic programming and develop therapeutic strategies to battle SARS-CoV-2.
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Affiliation(s)
- Mustafa Sertbas
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
| | - Kutlu O. Ulgen
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
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20
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Brady DK, Gurijala AR, Huang L, Hussain AA, Lingan AL, Pembridge OG, Ratangee BA, Sealy TT, Vallone KT, Clements TP. A guide to COVID-19 antiviral therapeutics: a summary and perspective of the antiviral weapons against SARS-CoV-2 infection. FEBS J 2024; 291:1632-1662. [PMID: 36266238 PMCID: PMC9874604 DOI: 10.1111/febs.16662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/11/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Antiviral therapies are integral in the fight against SARS-CoV-2 (i.e. severe acute respiratory syndrome coronavirus 2), the causative agent of COVID-19. Antiviral therapeutics can be divided into categories based on how they combat the virus, including viral entry into the host cell, viral replication, protein trafficking, post-translational processing, and immune response regulation. Drugs that target how the virus enters the cell include: Evusheld, REGEN-COV, bamlanivimab and etesevimab, bebtelovimab, sotrovimab, Arbidol, nitazoxanide, and chloroquine. Drugs that prevent the virus from replicating include: Paxlovid, remdesivir, molnupiravir, favipiravir, ribavirin, and Kaletra. Drugs that interfere with protein trafficking and post-translational processing include nitazoxanide and ivermectin. Lastly, drugs that target immune response regulation include interferons and the use of anti-inflammatory drugs such as dexamethasone. Antiviral therapies offer an alternative solution for those unable or unwilling to be vaccinated and are a vital weapon in the battle against the global pandemic. Learning more about these therapies helps raise awareness in the general population about the options available to them with respect to aiding in the reduction of the severity of COVID-19 infection. In this 'A Guide To' article, we provide an in-depth insight into the development of antiviral therapeutics against SARS-CoV-2 and their ability to help fight COVID-19.
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Affiliation(s)
- Drugan K. Brady
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Aashi R. Gurijala
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Liyu Huang
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Ali A. Hussain
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Audrey L. Lingan
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | | | - Brina A. Ratangee
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Tristan T. Sealy
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
| | - Kyle T. Vallone
- Department of Biological SciencesVanderbilt UniversityNashvilleTNUSA
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21
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Giri-Rachman EA, Effendy VV, Azmi MHS, Yamahoki N, Stephanie R, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Aditama R, Ningrum RA, Wardiana A, Fibriani A. The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential. ACS Synth Biol 2024; 13:509-520. [PMID: 38316139 PMCID: PMC10877612 DOI: 10.1021/acssynbio.3c00446] [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: 07/23/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (Mpro) dimer-based screening system (DBSS) utilizing synthetic biology in Escherichia coli BL21(DE3). We linked the SARS-CoV-2 Mpro with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-Mpro both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control (P ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 Mpro and also minimize the use of a high biosafety level laboratory.
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Affiliation(s)
| | - Vergio V. Effendy
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Muhammad H. S. Azmi
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Nicholas Yamahoki
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Rebecca Stephanie
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Dian F. Agustiyanti
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Popi H. Wisnuwardhani
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Marissa Angelina
- Research
Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency
(BRIN), Serpong 15314, Indonesia
| | - Yana Rubiyana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Reza Aditama
- Biochemistry
Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Ratih A. Ningrum
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Andri Wardiana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Azzania Fibriani
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
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22
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Saini R, Kumar V, Patel CN, Sourirajan A, Dev K. Synergistic antibacterial activity of Phyllanthus emblica fruits and its phytocompounds with ampicillin: a computational and experimental study. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:857-871. [PMID: 37522914 DOI: 10.1007/s00210-023-02624-0] [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: 06/03/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]
Abstract
Phyllanthus emblica L. (syn. Emblica officinalis), popularly known as amla, Indian gooseberry, or the King of Rasyana, is a member of Phyllanthaceae family and is traditionally used in Ayurveda as an immunity booster. The present study aimed to investigate the synergistic interaction of Phyllanthus emblica (FPE) fruits and its selected phytocompounds with ampicillin against selected bacteria. Further, an in silico technique was used to find if major phytocompounds of FPE could bind to proteins responsible for antibiotic resistance in bacterial pathogens and enhance the bioactivity of ampicillin. FPE and all the selected phytocompounds were found to have synergistic antibacterial activity with ampicillin against tested bacteria in different combinations. However, ellagic acid and quercetin interactions with ampicillin resulted in maximum bioactivity enhancement of 32-128 folds and 16-277 folds, respectively. In silico analysis revealed strong ellagic acid, quercetin, and rutin binding with penicillin-binding protein (PBP-) 3, further supported by MD simulations. Ellagic acid and quercetin also fulfill Lipinski's rule, showing similar toxicity characteristics to ampicillin. FPE showed synergistic interaction with ampicillin, possibly due to the presence of phytocompounds such as gallic acid, ellagic acid, quercetin, and rutin. Molecular docking and MD simulations showed the strong interaction of ellagic acid and quercetin with PBP-3 protein. Therefore, these compounds can be explored as potential non-toxic drug candidates to combat bacterial antimicrobial resistance.
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Affiliation(s)
- Rakshandha Saini
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, PO Sultanpur, Distt. Solan-173229 HP, Bajhol, India
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
| | - Chirag N Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, University School of Science, Gujarat University, Ahmedabad, Gujarat, 380009, India
- Biotechnology Research Center, Technology Innovation Institute, Masdar, Abu Dhabi, 9639, United Arab Emirates
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, PO Sultanpur, Distt. Solan-173229 HP, Bajhol, India
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, PO Sultanpur, Distt. Solan-173229 HP, Bajhol, India.
- Department of Pharmacology and Toxicology, Wright State University, Dayton, OH, 45435, USA.
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23
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Saha T, Lyons N, Yue Yung DB, Quiñones-Mateu ME, Pletzer D, Das SC. Repurposing ebselen as an inhalable dry powder to treat respiratory tract infections. Eur J Pharm Biopharm 2024; 195:114170. [PMID: 38128743 DOI: 10.1016/j.ejpb.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023]
Abstract
Respiratory tract infections (RTIs) are one of the leading causes of death globally, lately exacerbated by the increasing prevalence of antimicrobial resistance. While antimicrobial resistance could be overcome by developing new antimicrobial agents, the use of a safe repurposed agent having potent antimicrobial activity against various RTIs can be an efficient and cost-effective alternative to overcome the long and complex process of developing and testing new drugs. Ebselen, a synthetic organoselenium drug originally developed to treat noise-inducing hearing problems, has shown promising antimicrobial activity in vitro against several respiratory pathogens including viruses (e.g., SARS-CoV-2, influenza A virus) and bacteria (e.g., Mycobacterium tuberculosis, Streptococcus pneumoniae, and Staphylococcus aureus). Inhaled drug delivery is considered a promising approach for treating RTIs, as it can ensure effective drug concentrations at a lower dose, thereby minimizing the side effects that are often encountered by using oral or injectable drugs. In this study, we developed inhalable ebselen dry powder formulations using a spray-drying technique. The amino acids leucine, methionine, and tryptophan were incorporated with ebselen to enhance the yield and aerosolization of the dry powders. The amino acid-containing ebselen dry powders showed a better yield (37-56.4 %) than the amino acid-free formulation (30.9 %). All dry powders were crystalline in nature. The mass median aerodynamic diameter (MMAD) was less than 5 µm for amino acids containing dry powders (3-4 µm) and slightly higher (5.4 µm) for amino acid free dry powder indicating their suitability for inhalation. The aerosol performance was higher when amino acids were used, and the leucine-containing ebselen dry powder showed the highest emitted dose (84 %) and fine particle fraction (68 %). All amino acid formulations had similar cytotoxicity as raw ebselen, tested in respiratory cell line (A549 cells), with half-maximal inhibitory concentrations (IC50) between 100 and 250 μg/mL. Raw ebselen and amino acid-containing dry powders showed similar potent antibacterial activity against the Gram-positive bacteria S. aureus and S. pneumoniae with minimum inhibitory concentrations of 0.31 μg/mL and 0.16 μg/mL, respectively. On the other hand, raw ebselen and the formulations showed limited antimicrobial activity against the Gram-negative pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae. In summary, in this study we were able to develop amino-acid-containing inhalable dry powders of ebselen that could be used against different respiratory pathogens, especially Gram-positive bacteria, which could ensure more drug deposition in the respiratory tract, including the lungs. DPIs are generally used to treat lung (lower respiratory tract) diseases. However, DPIs can also be used to treat both upper and lower RTIs. The deposition of the dry powder in the respiratory tract is dependent on its physicochemical properties and this properties can be modulated to target the intended site of infection (upper and/or lower respiratory tract). Further studies will allow the development of similar formulations of individual and/or combination of antimicrobials that could be used to inhibit a number of respiratory pathogens.
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Affiliation(s)
- Tushar Saha
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Nikita Lyons
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Deborah Bow Yue Yung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniel Pletzer
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Shyamal C Das
- School of Pharmacy, University of Otago, Dunedin, New Zealand.
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24
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Waseem W, Zafar R, Jan MS, Alomar TS, Almasoud N, Rauf A, Khattak H. Drug repurposing of FDA-approved anti-viral drugs via computational screening against novel 6M03 SARS-COVID-19. Ir J Med Sci 2024; 193:73-83. [PMID: 37515684 DOI: 10.1007/s11845-023-03473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023]
Abstract
OBJECTIVE The COVID-19 pandemic has been recognized as severe acute respiratory syndrome, one of the worst and disastrous infectious diseases in human history. Until now, there is no cure to this contagious infection although some multinational pharmaceutical companies have synthesized the vaccines and injecting them into humans, but a drug treatment regimen is yet to come. AIM Among the multiple areas of SARS-CoV-2 that can be targeted, protease protein has significant values due to its essential role in viral replication and life. The repurposing of FDA-approved drugs for the treatment of COVID-19 has been a critical strategy during the pandemic due to the urgency of effective therapies. The novelty in this work refers to the innovative use of existing drugs with greater safety, speed, cost-effectiveness, broad availability, and diversity in the mechanism of action that have been approved and developed for other medical conditions. METHODS In this research work, we have engaged drug reprofiling or drug repurposing to recognize possible inhibitors of protease protein 6M03 in an instantaneous approach through computational docking studies. RESULTS We screened 16 FDA-approved anti-viral drugs that were known for different viral infections to be tested against this contagious novel strain. Through these reprofiling studies, we come up with 5 drugs, namely, Delavirdine, Fosamprenavir, Imiquimod, Stavudine, and Zanamivir, showing excellent results with the negative binding energies in Kcal/mol as - 8.5, - 7.0, - 6.8, - 6.8, and - 6.6, respectively, in the best binding posture. In silico studies allowed us to demonstrate the potential role of these drugs against COVID-19. CONCLUSION In our study, we also observed the nucleotide sequence of protease protein consisting of 316 amino acid residues and the influence of these pronouncing drugs over these sequences. The outcome of this research work provides researchers with a track record for carrying out further investigational procedures by applying docking simulations and in vitro and in vivo experimentation with these reprofile drugs so that a better drug can be formulated against coronavirus.
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Affiliation(s)
- Wajeeha Waseem
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore Campus, Lahore, 54000, Pakistan
| | - Rehman Zafar
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Riphah International University, Islamabad, 44000, Pakistan
| | - Muhammad Saeed Jan
- Department of Pharmacy, Bacha Khan University Charsadda, Charsadda, 24420, KP, Pakistan.
| | - Taghrid S Alomar
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84427, 11671, Riyadh, Saudi Arabia.
| | - Najla Almasoud
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84427, 11671, Riyadh, Saudi Arabia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, 23430, Anbar, Pakistan.
| | - Humayoon Khattak
- Department of Pharmacy, Bacha Khan University Charsadda, Charsadda, 24420, KP, Pakistan
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25
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Li Y, Ma H. Drug repurposing: insights into the antimicrobial effects of AKBA against MRSA. AMB Express 2024; 14:5. [PMID: 38184513 PMCID: PMC10771487 DOI: 10.1186/s13568-024-01660-0] [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: 11/04/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024] Open
Abstract
Staphylococcus aureus is a major threat in infectious diseases due to its varied infection types and increased resistance. S. aureus could form persister cells under certain condition and could also attach on medical apparatus to form biofilms, which exhibited extremely high resistance to antibiotics. 3-Acetyl-11-keto-beta-boswellic acid (AKBA) is a well-studied anti-tumor and antioxidant drug. This study is aimed to determine the antimicrobial effects of AKBA against S. aureus and its persister cells and biofilms. The in vitro antimicrobial susceptibility of AKBA was assessed by micro-dilution assay, disc diffusion assay and time-killing assay. Drug combination between AKBA and conventional antibiotics was detected by checkerboard assay. And the antibiofilm effects of AKBA against S. aureus were explored by crystal violet staining combined with SYTO/PI probes staining. Next, RBC lysis activity and CCK-8 kit were used to determine the cytotoxicity of AKBA. In addition, murine subcutaneous abscess model was used to assess the antimicrobial effects of AKBA in vivo. Our results revealed that AKBA was found to show effective antimicrobial activity against methicillin-resistant S. aureus (MRSA) with the minimal inhibitory concentration of 4-8 µg/mL with undetectable cytotoxicity. And no resistant mutation was induced by AKBA after 20 days of consecutive passage. Further, we found that AKBA could be synergy with gentamycin or amikacin against S. aureus and its clinical isolates. By crystal violet and SYTO9/PI staining, AKBA exhibited strong biofilm inhibitory and eradication effects at the concentration of 1 ~ 4 µg/mL. In addition, the effective antimicrobial effect was verified in vivo in a mouse model. And no detectable in vivo toxicity was found. These results indicated that AKBA has great potential to development as an alternative treatment for the refractory S. aureus infections.
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Affiliation(s)
- Yingjia Li
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Hongbing Ma
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China.
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26
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Mandal SK, Rehman MDMU, Katyal A, Rajvanshi K, Kannan M, Garg M, Murugesan S, Deepa P. In silico anti-viral assessment of phytoconstituents in a traditional (Siddha Medicine) polyherbal formulation - Targeting Mpro and pan-coronavirus post-fusion Spike protein. J Tradit Complement Med 2024; 14:55-69. [PMID: 38223813 PMCID: PMC10785248 DOI: 10.1016/j.jtcme.2023.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 01/16/2024] Open
Abstract
Background and aim Novel nature of the viral pathogen SARS-CoV-2 and the absence of standard drugs for treatment, have been a major challenge to combat this deadly infection. Natural products offer safe and effective remedy, for which traditional ethnic medicine can provide leads. An indigenous poly-herbal formulation, Kabasura Kudineer from Siddha system of medicine was evaluated here using a combination of computational approaches, to identify potential inhibitors against two anti-SARS-CoV-2 targets - post-fusion Spike protein (structural protein) and main protease (Mpro, non-structural protein). Experimental procedure We docked 32 phytochemicals from the poly-herbal formulation against viral post-fusion Spike glycoprotein and Mpro followed by molecular dynamics using Schrodinger software. Drug-likeness analysis was performed using machine learning (ML) approach and pkCSM. Results The binding affinity of the phytochemicals in Kabasura Kudineer revealed the following top-five bioactives: Quercetin > Luteolin > Chrysoeriol > 5-Hydroxy-7,8-Dimethoxyflavone > Scutellarein against Mpro target, and Gallic acid > Piperlonguminine > Chrysoeriol > Elemol > Piperine against post-fusion Spike protein target. Quercetin and Gallic acid exhibited binding stability in complexation with their respective viral-targets and favourable free energy change as revealed by the molecular dynamics simulations and MM-PBSA analysis. In silico predicted pharmacokinetic profiling of these ligands revealed appropriate drug-likeness properties. Conclusion These outcomes provide: (a) potential mechanism for the anti-viral efficacy of the indigenous Siddha formulation, targeting Mpro and post-fusion Spike protein (b) top bioactive lead-molecules that may be developed as natural product-based anti-viral pharmacotherapy and their pleiotropic protective effects may be leveraged to manage co-morbidities associated with COVID-19.
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Affiliation(s)
- Sumit Kumar Mandal
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - MD Muzaffar-Ur Rehman
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Ashish Katyal
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Kanishk Rajvanshi
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Manoj Kannan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
- Plaksha University, SAS Nagar, Mohali, 140306, Punjab, India
| | - Mohit Garg
- Department of Chemical Engineering, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - P.R. Deepa
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
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Dinata R, Nisa N, Arati C, Rasmita B, Uditraj C, Siddhartha R, Bhanushree B, Saeed-Ahmed L, Manikandan B, Bidanchi RM, Abinash G, Pori B, Khushboo M, Roy VK, Gurusubramanian G. Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods. J Biomol Struct Dyn 2024; 42:43-81. [PMID: 37021347 DOI: 10.1080/07391102.2023.2192797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
The COVID-19 pandemic has caused adverse health (severe respiratory, enteric and systemic infections) and environmental impacts that have threatened public health and the economy worldwide. Drug repurposing and small molecule multi-target directed herbal medicine therapeutic approaches are the most appropriate exploration strategies for SARS-CoV-2 drug discovery. This study identified potential multi-target-directed Parkia bioactive entities against SARS-CoV-2 receptors (S-protein, ACE2, TMPRSS2, RBD/ACE2, RdRp, MPro, and PLPro) using ADMET, drug-likeness, molecular docking (AutoDock, FireDock and HDOCK), molecular dynamics simulation and MM-PBSA tools. One thousand Parkia bioactive entities were screened out by virtual screening and forty-five bioactive phytomolecules were selected based on favorable binding affinity and acceptable pharmacokinetic and pharmacodynamics properties. The binding affinity values of Parkia phyto-ligands (AutoDock: -6.00--10.40 kcal/mol; FireDock: -31.00--62.02 kcal/mol; and HDOCK: -150.0--294.93 kcal/mol) were observed to be higher than the reference antiviral drugs (AutoDock: -5.90--9.10 kcal/mol; FireDock: -35.64--59.35 kcal/mol; and HDOCK: -132.82--211.87 kcal/mol), suggesting a potent modulatory action of Parkia bioactive entities against the SARS-CoV-2. Didymin, rutin, epigallocatechin gallate, epicatechin-3-0-gallate, hyperin, ursolic acid, lupeol, stigmasta-5,24(28)-diene-3-ol, ellagic acid, apigenin, stigmasterol, and campesterol strongly bound with the multiple targets of the SARS-CoV-2 receptors, inhibiting viral entry, attachment, binding, replication, transcription, maturation, packaging and spread. Furthermore, ACE2, TMPRSS2, and MPro receptors possess significant molecular dynamic properties, including stability, compactness, flexibility and total binding energy. Residues GLU-589, and LEU-95 of ACE2, GLN-350, HIS-186, and ASP-257 of TMPRSS2, and GLU-14, MET-49, and GLN-189 of MPro receptors contributed to the formation of hydrogen bonds and binding interactions, playing vital roles in inhibiting the activity of the receptors. Promising results were achieved by developing multi-targeted antiviral Parkia bioactive entities as lead and prospective candidates under a small molecule strategy against SARS-CoV-2 pathogenesis. The antiviral activity of Parkia bioactive entities needs to be further validated by pre-clinical and clinical trials.
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Affiliation(s)
- Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | | | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Maurya Khushboo
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
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Farghaly TA, Masaret GS, Riyadh SM, Harras MF. A Literature Review Focusing on the Antiviral Activity of [1,2,4] and [1,2,3]-triazoles. Mini Rev Med Chem 2024; 24:1602-1629. [PMID: 38008942 DOI: 10.2174/0113895575277122231108095511] [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: 08/12/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 11/28/2023]
Abstract
Out of a variety of heterocycles, triazole scaffolds have been shown to play a significant part in a wide array of biological functions. Many drug compounds containing a triazole moiety with important antimicrobial, anticancer and antidepressant properties have been commercialized. In addition, the triazole scaffold exhibits remarkable antiviral activity either incorporated into nucleoside analogs or non-nucleosides. Many synthetic techniques have been produced by scientists around the world as a result of their wide-ranging biological function. In this review, we have tried to summarize new synthetic methods produced by diverse research groups as well as provide a comprehensive description of the function of [1,2,4] and [1,2,3]-triazole derivatives as antiviral agents. Antiviral triazole compounds have been shown to target a wide variety of molecular proteins. In addition, several strains of viruses, including the human immunodeficiency virus, SARS virus, hepatitis B and C viruses, influenza virus, Hantavirus, and herpes virus, were discovered to be susceptible to triazole derivatives. This review article covered the reports for antiviral activity of both 1,2,3- and 1,2,4-triazole moieties up to 2022.
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Affiliation(s)
- Thoraya A Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah Almukaramah, 21514, Saudi Arabia
| | - Ghada S Masaret
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah Almukaramah, 21514, Saudi Arabia
| | - Sayed M Riyadh
- Chemistry Department, Faculty of Science, University of Cairo, Giza 12613, Egypt
| | - Marwa F Harras
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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Zhao H, Li H, Liu Q, Dong G, Hou C, Li Y, Zhao Y. Using TransR to enhance drug repurposing knowledge graph for COVID-19 and its complications. Methods 2024; 221:82-90. [PMID: 38104883 DOI: 10.1016/j.ymeth.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
MOTIVATION The COVID-19 pandemic has been spreading globally for four years, yet specific drugs that effectively suppress the virus remain elusive. Furthermore, the emergence of complications associated with COVID-19 presents significant challenges, making the development of therapeutics for COVID-19 and its complications an urgent task. However, traditional drug development processes are time-consuming. Drug repurposing, which involves identifying new therapeutic applications for existing drugs, presents a viable alternative. RESULT In this study, we construct a knowledge graph by retrieving information on genes, drugs, and diseases from databases such as DRUGBANK and GNBR. Next, we employ the TransR knowledge representation learning approach to embed entities and relationships into the knowledge graph. Subsequently, we train the knowledge graph using a graph neural network model based on TransR scoring. This trained knowledge graph is then utilized to predict drugs for the treatment of COVID-19 and its complications. Based on experimental results, we have identified 15 drugs out of the top 30 with the highest success rates associated with treating COVID-19 and its complications. Notably, out of these 15 drugs, 10 specifically aimed at treating COVID-19, such as Torcetrapib and Tocopherol, has not been previously identified in the knowledge graph. This finding highlights the potential of our model in aiding healthcare professionals in drug development and research related to this disease.
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Affiliation(s)
- Hongxi Zhao
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Hongfei Li
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Qiaoming Liu
- School of Medicine and Health, Harbin Institute of Technology, 150001, Harbin, HeiLongJiang, China; Zhengzhou Research Institute, Harbin Institute of Technology, 450000, Zhengzhou, Henan, China
| | - Guanghui Dong
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Chang Hou
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Yang Li
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.
| | - Yuming Zhao
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.
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Manchanda RK, Miglani A, Kalsi A, Brahmachari S, Rama KN, Goel P, Kaushik P, Jethani A, Nagrath C, Pangtey NY, Kannoth JT, Sharma K, Arora S, Amitav B, Roy PK, Kudiyarasu RK, Rutten L. Homeopathic Medicines in Third (Omicron) Wave of COVID-19: Prognostic Factor Research. HOMEOPATHY 2023. [PMID: 38158196 DOI: 10.1055/s-0043-1776758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
BACKGROUND With the emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, such as the Omicron variant, during the third wave of the coronavirus disease 2019 (COVID-19) pandemic, there was a need to identify useful homeopathic medicines. This study aimed to identify such medicines and their indications using prognostic factor research (PFR). METHODS This was an open-label, multi-centred observational study conducted in January 2022, on confirmed COVID-19 cases. The data were collected from integrated COVID Care Centres in Delhi, India, where homeopathic medicines were prescribed along with conventional treatment. Only those cases that met a set of selection criteria were considered for analysis. The likelihood ratio (LR) was calculated for the frequently occurring symptoms of the frequently prescribed medicines. An LR of 1.3 or greater was considered meaningful. RESULTS Out of the 362 COVID-19 cases, 263 cases were selected for analysis after applying selection criteria. Common symptoms included fatigue, cough, sore throat, myalgia and headache. Twenty-one medicines were prescribed, of which nine medicines - Gelsemium sempervirens, Bryonia alba, Hepar sulphuris, Rhus toxicodendron, Pulsatilla nigricans, Arsenicum album, Belladonna, Nux vomica and Phosphorus - were frequently used. By calculating LRs, the study identified meaningful indications for these medicines. CONCLUSION Homeopathic medicines have shown promising results in the third wave of COVID-19 as an adjunct therapy. The medicines that were used in the first and second waves were found useful in the third wave also, and their indications were analogous to those found in the earlier waves. Certain new indications of some medicines were elicited in this wave, which warrant further research. However, it is important not to restrict to these medicines only and to continue data collection on COVID-19 in future waves for the improvement of the COVID-19 mini-repertory.
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Affiliation(s)
- Raj Kumar Manchanda
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, Secretary for Information and Communication, Liga Medicorum Homeopathica Internationalis, New Delhi, India
| | - Anjali Miglani
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Amrit Kalsi
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Smita Brahmachari
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Kamsali Nadigadda Rama
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Pawan Goel
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Pallavi Kaushik
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Anju Jethani
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Cheshta Nagrath
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Nirmal Yadav Pangtey
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Jithesh Thavarayil Kannoth
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Kavita Sharma
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Shelly Arora
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - B Amitav
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Pradip Kumar Roy
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Ram Kumar Kudiyarasu
- Health and Family Welfare Department, Directorate of AYUSH, Government of National Capital Territory of Delhi, New Delhi, India
| | - Lex Rutten
- Independent Practitioner, Breda, The Netherlands
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Zhang B, Yu J, Zhu G, Huang Y, Zhang K, Xiao X, He W, Yuan J, Gao X. Dapoxetine, a Selective Serotonin Reuptake Inhibitor, Suppresses Zika Virus Infection In Vitro. Molecules 2023; 28:8142. [PMID: 38138628 PMCID: PMC10745718 DOI: 10.3390/molecules28248142] [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: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Zika virus (ZIKV) belongs to the Flavivirus genus of the Flaviviridae family, and is a pathogen posing a significant threat to human health. Currently, there is a lack of internationally approved antiviral drugs for the treatment of ZIKV infection, and symptomatic management remains the primary clinical approach. Consequently, the exploration of safe and effective anti-ZIKV drugs has emerged as a paramount imperative in ZIKV control efforts. In this study, we performed a screening of a compound library consisting of 1789 FDA-approved drugs to identify potential agents with anti-ZIKV activity. We have identified dapoxetine, an orally administered selective serotonin reuptake inhibitor (SSRI) commonly employed for the clinical management of premature ejaculation (PE), as a potential inhibitor of ZIKV RNA-dependent RNA polymerase (RdRp). Consequently, we conducted surface plasmon resonance (SPR) analysis to validate the specific binding of dapoxetine to ZIKV RdRp, and further evaluated its inhibitory effect on ZIKV RdRp synthesis using the ZIKV Gluc reporter gene assay. Furthermore, we substantiated the efficacy of dapoxetine in suppressing intracellular replication of ZIKV, thereby demonstrating a concentration-dependent antiviral effect (EC50 values ranging from 4.20 μM to 12.6 μM) and negligible cytotoxicity (CC50 > 50 μM) across diverse cell lines. Moreover, cell fluorescence staining and Western blotting assays revealed that dapoxetine effectively reduced the expression of ZIKV proteins. Collectively, our findings suggest that dapoxetine exhibits anti-ZIKV effects by inhibiting ZIKV RdRp activity, positioning it as a potential candidate for clinical therapeutic intervention against ZIKV infection.
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Affiliation(s)
- Bingzhi Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China;
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
| | - Jianchen Yu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
| | - Ge Zhu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yun Huang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China;
| | - Kexin Zhang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China;
| | - Xuhan Xiao
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenxuan He
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China;
| | - Jie Yuan
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China;
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Khan K, Jalal K, Uddin R. Pangenome diversification and resistance gene characterization in Salmonella Typhi prioritized RfaJ as a significant therapeutic marker. J Genet Eng Biotechnol 2023; 21:125. [PMID: 37975995 PMCID: PMC10656401 DOI: 10.1186/s43141-023-00591-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Salmonella Typhi stands as the etiological agent responsible for the onset of human typhoid fever. The pressing demand for innovative therapeutic targets against S. Typhi is underscored by the escalating prevalence of this pathogen and the severe nature of its infections. Consequently, this study employs pangenome analysis to scrutinize 119 S. Typhi-resistant strains, aiming to identify the most promising therapeutic targets originating from its core genome. RESULTS Subtractive genomics was employed to systematically eliminate non-homologous (n=1147), essential (n=551), drug-like (n=80), and pathogenicity-related (n=18) proteins from the initial pool of 3351 core genome proteins. Consequently, lipopolysaccharide 1,2-glucosyltransferase RfaJ was designated as the optimal pharmacological target due to its potential versatility. Furthermore, a compendium of 9000 FDA-approved compounds was repurposed for evaluation against the RfaJ drug target, with the specific intent of prioritizing novel, high-potency therapeutic candidates for combating S. Typhi. Ultimately, four compounds, namely DB00549 (Zafirlukast), DB15637 (Fluzoparib), DB15688 (Zavegepant), and DB12411 (Bemcentinib), were singled out as potential inhibitors based on the ligand-protein binding affinity (indicated by the lowest anticipated binding energy) and the overall stability of these compounds. Notably, molecular dynamics simulations, conducted over a 50 nanosecond interval, convincingly demonstrated the stability of these compounds in the context of the RfaJ protein. CONCLUSION In summary, the present findings hold significant promise as an initial stride in the broader drug discovery endeavor against S. Typhi infections. However, the experimental validation of the identified drug target and drug candidate is further required to increase the effectiveness of the applied methodology.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
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Pavithran H, Kumavath R, Ghosh P. Transcriptome Profiling of Cardiac Glycoside Treatment Reveals EGR1 and Downstream Proteins of MAPK/ERK Signaling Pathway in Human Breast Cancer Cells. Int J Mol Sci 2023; 24:15922. [PMID: 37958905 PMCID: PMC10647710 DOI: 10.3390/ijms242115922] [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: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Cardiac glycosides (CGs) constitute a group of steroid-like compounds renowned for their effectiveness in treating cardiovascular ailments. In recent times, there has been growing recognition of their potential use as drug leads in cancer treatment. In our prior research, we identified three highly promising CG compounds, namely lanatoside C (LC), peruvoside (PS), and strophanthidin (STR), which exhibited significant antitumor effects in lung, liver, and breast cancer cell lines. In this study, we investigated the therapeutic response of these CGs, with a particular focus on the MCF-7 breast cancer cell line. We conducted transcriptomic profiling and further validated the gene and protein expression changes induced by treatment through qRT-PCR, immunoblotting, and immunocytochemical analysis. Additionally, we demonstrated the interactions between the ligands and target proteins using the molecular docking approach. The transcriptome analysis revealed a cluster of genes with potential therapeutic targets involved in cytotoxicity, immunomodulation, and tumor-suppressor pathways. Subsequently, we focused on cross-validating the ten most significantly expressed genes, EGR1, MAPK1, p53, CCNK, CASP9, BCL2L1, CDK7, CDK2, CDK2AP1, and CDKN1A, through qRT-PCR, and their by confirming the consistent expression pattern with RNA-Seq data. Notably, among the most variable genes, we identified EGR1, the downstream effector of the MAPK signaling pathway, which performs the regulatory function in cell proliferation, tumor invasion, and immune regulation. Furthermore, we substantiated the influence of CG compounds on translational processes, resulting in an alteration in protein expression upon treatment. An additional analysis of ligand-protein interactions provided further evidence of the robust binding affinity between LC, PS, and STR and their respective protein targets. These findings underscore the intense anticancer activity of the investigated CGs, shedding light on potential target genes and elucidating the probable mechanism of action of CGs in breast cancer.
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Affiliation(s)
- Honey Pavithran
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod 671320, India;
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod 671320, India;
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA;
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Liao X, Ozcan M, Shi M, Kim W, Jin H, Li X, Turkez H, Achour A, Uhlén M, Mardinoglu A, Zhang C. Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy. Bioinformatics 2023; 39:btad666. [PMID: 37930015 PMCID: PMC10637856 DOI: 10.1093/bioinformatics/btad666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023] Open
Abstract
MOTIVATION Many approaches in systems biology have been applied in drug repositioning due to the increased availability of the omics data and computational biology tools. Using a multi-omics integrated network, which contains information of various biological interactions, could offer a more comprehensive inspective and interpretation for the drug mechanism of action (MoA). RESULTS We developed a computational pipeline for dissecting the hidden MoAs of drugs (Open MoA). Our pipeline computes confidence scores to edges that represent connections between genes/proteins in the integrated network. The interactions showing the highest confidence score could indicate potential drug targets and infer the underlying molecular MoAs. Open MoA was also validated by testing some well-established targets. Additionally, we applied Open MoA to reveal the MoA of a repositioned drug (JNK-IN-5A) that modulates the PKLR expression in HepG2 cells and found STAT1 is the key transcription factor. Overall, Open MoA represents a first-generation tool that could be utilized for predicting the potential MoA of repurposed drugs and dissecting de novo targets for developing effective treatments. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/XinmengLiao/Open_MoA.
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Affiliation(s)
- Xinmeng Liao
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Mehmet Ozcan
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
- Department of Medical Biochemistry, Faculty of Medicine, Zonguldak Bulent Ecevit University, 67630 Zonguldak, Turkey
| | - Mengnan Shi
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Woonghee Kim
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Han Jin
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Xiangyu Li
- Guangzhou National Laboratory, Guangzhou, Guangdong Province 510005, China
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum 25240, Turkey
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, 17176 Stockholm, Sweden
| | - Mathias Uhlén
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, United Kingdom
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
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Saha T, Sinha S, Harfoot R, Quiñones-Mateu ME, Das SC. Inhalable dry powder containing remdesivir and disulfiram: Preparation and in vitro characterization. Int J Pharm 2023; 645:123411. [PMID: 37703955 DOI: 10.1016/j.ijpharm.2023.123411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
The respiratory tract, as the first and most afflicted target of many viruses such as SARS-CoV-2, seems to be the logical choice for delivering antiviral agents against this and other respiratory viruses. A combination of remdesivir and disulfiram, targeting two different steps in the viral replication cycle, has showed synergistic activity against SARS-CoV-2 in-vitro. In this study, we have developed an inhalable dry powder containing a combination of remdesivir and disulfiram utilizing the spray-drying technique, with the final goal of delivering this drug combination to the respiratory tract. The prepared dry powders were spherical, and crystalline. The particle size was between 1 and 5 μm indicating their suitability for inhalation. The spray-dried combinational dry powder containing remdesivir and disulfiram (RDSD) showed a higher emitted dose (ED) of >88% than single dry powder of remdesivir (RSD) (∼72%) and disulfiram (DSD) (∼84%), with a fine particle fraction (FPF) of ∼55%. Addition of L-leucine to RDSD showed >60% FPF with a similar ED. The in vitro aerosolization was not significantly affected after the stability study conducted at different humidity conditions. Interestingly, the single (RSD and DSD) and combined (RDSD) spray-dried powders showed limited cellular toxicity (CC50 values from 39.4 to >100 µM), while maintaining their anti-SARS-CoV-2 in vitro (EC50 values from 4.43 to 6.63 µM). In a summary, a combinational dry powder formulation containing remdesivir and disulfiram suitable for inhalation was developed by spray-drying technique which showed high cell viability in the respiratory cell line (Calu-3 cells) retaining their anti-SARS-CoV-2 property. In the future, in vivo studies will test the ability of these formulations to inhibit SARS-CoV-2 which is essential for clinical translation.
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Affiliation(s)
- Tushar Saha
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Shubhra Sinha
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Miguel E Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Shyamal C Das
- School of Pharmacy, University of Otago, Dunedin, New Zealand.
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Al-Wahaibi LH, Rehman MT, Al-Saleem MSM, Basudan OA, El-Gamal AA, Abdelkader MSA, AlAjmi MF, Abdel-Mageed WM. Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID-19 virus main protease and spike protein. J Biomol Struct Dyn 2023; 41:8961-8977. [PMID: 36300522 DOI: 10.1080/07391102.2022.2139295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 10/31/2022]
Abstract
The lack of any effective cure for the infectious COVID-19 disease has created a sense of urgency and motivated the search for effective antiviral drugs. Abyssomicins are actinomyces-derived spirotetronates polyketides antibiotics known for their promising antibacterial, antitumor, and antiviral activities. In this study, computational approaches were used to investigate the binding mechanism and the inhibitory ability of 38 abyssomicins against the main protease (Mpro) and the spike protein receptor-binding domain (RBD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The results identified abyssomicins C, J, W, atrop-O-benzyl abyssomicin C, and atrop-O-benzyl desmethyl abyssomicin C as the most potential inhibitors of Mpro and RBD with binding energy ranges between -8.1 and -9.9 kcal mol-1; and between -6.9 and -8.2 kcal mol-1, respectively. Further analyses of physicochemical properties and drug-likeness suggested that all selected active abyssomicins, with the exception of abyssomicin J, obeyed Lipinski's rule of five. The stability of protein-ligand complexes was confirmed by performing molecular dynamics simulation for 100 ns and evaluating parameters such as such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), total number of contacts, and secondary structure. Prime/MM-GBSA (Molecular Mechanics-General Born Surface Area) and principal component analysis (PCA) analyses also confirmed the stable nature of protein-ligand complexes. Overall, the results showed that the studied abyssomicins have significant interactions with the selected protein targets; therefore, they were deemed viable candidates for further in vitro and in vivo evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muneera S M Al-Saleem
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Omer A Basudan
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali A El-Gamal
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, El Mansoura, Egypt
| | | | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Wael M Abdel-Mageed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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Boopathi V, Nahar J, Murugesan M, Subramaniyam S, Kong BM, Choi SK, Lee CS, Ling L, Yang DU, Yang DC, Mathiyalagan R, Chan Kang S. In silico and in vitro inhibition of host-based viral entry targets and cytokine storm in COVID-19 by ginsenoside compound K. Heliyon 2023; 9:e19341. [PMID: 37809955 PMCID: PMC10558348 DOI: 10.1016/j.heliyon.2023.e19341] [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: 11/02/2022] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus that emerged as an epidemic, causing a respiratory disease with multiple severe symptoms and deadly consequences. ACE-2 and TMPRSS2 play crucial and synergistic roles in the membrane fusion and viral entry of SARS-CoV-2 (COVID-19). The spike (S) protein of SARS-CoV-2 binds to the ACE-2 receptor for viral entry, while TMPRSS2 proteolytically cleaves the S protein into S1 and S2 subunits, promoting membrane fusion. Therefore, ACE-2 and TMPRSS2 are potential drug targets for treating COVID-19, and their inhibition is a promising strategy for treatment and prevention. This study proposes that ginsenoside compound K (G-CK), a triterpenoid saponin abundant in Panax Ginseng, a dietary and medicinal herb highly consumed in Korea and China, effectively binds to and inhibits ACE-2 and TMPRSS2 expression. We initially conducted an in-silico evaluation where G-CK showed a high affinity for the binding sites of the two target proteins of SARS-CoV-2. Additionally, we evaluated the stability of G-CK using molecular dynamics (MD) simulations for 100 ns, followed by MM-PBSA calculations. The MD simulations and free energy calculations revealed that G-CK has stable and favorable energies, leading to strong binding with the targets. Furthermore, G-CK suppressed ACE2 and TMPRSS2 mRNA expression in A549, Caco-2, and MCF7 cells at a concentration of 12.5 μg/mL and in LPS-induced RAW 264.7 cells at a concentration of 6.5 μg/mL, without significant cytotoxicity.ACE2 and TMPRSS2 expression were significantly lower in A549 and RAW 264.7 cells following G-CK treatment. These findings suggest that G-CK may evolve as a promising therapeutic against COVID-19.
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Affiliation(s)
- Vinothini Boopathi
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Jinnatun Nahar
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Mohanapriya Murugesan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | | | - Byoung Man Kong
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Sung-Keun Choi
- Daedong Korea Ginseng Co., Ltd, 86, Gunbuk-ro, Gunbuk-myeon, Geumsan-gun, Chungcheongnam-do 32718 Republic of Korea
| | - Chang-Soon Lee
- Daedong Korea Ginseng Co., Ltd, 86, Gunbuk-ro, Gunbuk-myeon, Geumsan-gun, Chungcheongnam-do 32718 Republic of Korea
| | - Li Ling
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Dong Uk Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Deok Chun Yang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Se Chan Kang
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
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Kumar A, Kalra S, Jangid K, Jaitak V. Flavonoids as P-glycoprotein inhibitors for multidrug resistance in cancer: an in-silico approach. J Biomol Struct Dyn 2023; 41:7627-7639. [PMID: 36120941 DOI: 10.1080/07391102.2022.2123390] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Cancer has become a leading cause of mortality due to non-communicable diseases after cardiovascular disease worldwide and is increasing day by day at a daunting pace. According to an estimate by 2040 there will be 28.4 million cancer cases. Occurrence of multidrug resistance has further worsened the scenario of available cancer treatment. Among different mechanisms of multidrug resistance efflux of xenobiotics by ABC transporter is of prime importance. P-glycoprotein (P-gp) is the major factor behind occurrence of multidrug resistance due to its wide distribution and invariably big binding cavity. Various generations of chemical inhibitors for P-gp have been designed and tested are not devoid of major side effects. Thus, in present study flavonoids a major class of natural compounds was virtually screened in order to find molecules which can be used as selective P-gp inhibitors to be used along with chemotherapeutics. After screening 4275 molecules from different classes of flavonoids i.e. flavan, flavanol, flavonone, flavone, anthocyanins, and isoflavone, through Glide docking top ten hit molecules were selected based on their binding affinity, binding energy calculation and pharmacokinetic properties. All the hit molecules were found to have docking score within the range of -11.202 to -9.699 kcal/mol showing very strong interaction with the amino acid residues of binding pocket. Whereas, dock score of standard P-gp inhibitor verapamil was -4.984 kcal/mol. The ligand and protein complex were found to be quite stable while run through molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Kumar
- Laboratory of Natural Product Chemistry, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
| | - Sourav Kalra
- School of Pharmacy, Chitkara University, Baddi, Himachal Pradesh, India
| | - Kailash Jangid
- Department of Pharmacy, School of Chemical Sciences & Pharmacy, Central University of Rajasthan, Ajmer, India
| | - Vikas Jaitak
- Laboratory of Natural Product Chemistry, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, India
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Ugurel E, Turgut-Balik D. Synergistic combination of carvedilol, amlodipine, amitriptyline, and antibiotics as an alternative treatment approach for the susceptible and multidrug-resistant A. baumannii infections via drug repurposing. Eur J Clin Microbiol Infect Dis 2023; 42:1063-1072. [PMID: 37428238 DOI: 10.1007/s10096-023-04634-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 07/11/2023]
Abstract
We evaluated in vitro activity of 13 drugs used in the treatment of some non-communicable diseases via repurposing to determine their potential use in the treatment of Acinetobacter baumannii infections caused by susceptible and multidrug-resistant strains. A. baumannii is a multidrug-resistant Gram-negative bacteria causing nosocomial infections, especially in intensive care units. It has been identified in the WHO critical pathogen list and this emphasises urgent need for new treatment options. As the development of new therapeutics is expensive and time consuming, finding new uses of existing drugs via drug repositioning has been favoured. Antimicrobial susceptibility tests were conducted on all 13 drugs according to CLSI. Drugs with MIC values below 128 μg/mL and control antibiotics were further subjected to synergetic effect and bacterial time-kill analysis. Carvedilol-gentamicin (FICI 0.2813) and carvedilol-amlodipine (FICI 0.5625) were determined to have synergetic and additive effect, respectively, on the susceptible A. baumannii strain, and amlodipine-tetracycline (FICI 0.75) and amitriptyline-tetracycline (FICI 0.75) to have additive effect on the multidrug-resistant A. baumannii strain. Most remarkably, both amlodipine and amitriptyline reduced the MIC of multidrug-resistant, including some carbapenems, A. baumannii reference antibiotic tetracycline from 2 to 0.5 μg/mL, for 4-folds. All these results were further supported by bacterial time-kill assay and all combinations showed bactericidal activity, at certain hours, at 4XMIC. Combinations proposed in this study may provide treatment options for both susceptible and multidrug-resistant A. baumannii infections but requires further pharmacokinetics and pharmacodynamics analyses and in vivo re-evaluations using appropriate models.
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Affiliation(s)
- Erennur Ugurel
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Davutpasa Campus, 34210, Esenler, Istanbul, Türkiye
| | - Dilek Turgut-Balik
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Davutpasa Campus, 34210, Esenler, Istanbul, Türkiye.
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40
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Mandal N, Rath SL. Identification of inhibitors against SARS-CoV-2 variants of concern using virtual screening and metadynamics-based enhanced sampling. Chem Phys 2023; 573:111995. [PMID: 37342284 PMCID: PMC10265933 DOI: 10.1016/j.chemphys.2023.111995] [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: 02/01/2023] [Revised: 05/12/2023] [Accepted: 06/11/2023] [Indexed: 06/22/2023]
Abstract
Among the variants of SARS-CoV-2, some are more infectious than the Wild-type. Interestingly, these mutations enable the virus to evade the therapeutic efforts. Hence, there is a need for candidate drug molecules that can potently bind with all the variants. We have adopted a strategy combining virtual screening, molecular docking followed by rigorous sampling by metadynamics simulations to find candidate molecules. From our results we found four highly potent drug candidates that can bind to the Spike-RBD of all the variants of the virus. Additionally, we also found that certain signature residues on the RBM region commonly bind to each of these inhibitors. Thus, our study not only gives information on the chemical compounds, but also residues on the proteins which could be targeted for future drug and vaccine development studies.
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Affiliation(s)
- Nabanita Mandal
- Department of Biotechnology, National Institute of Technology Warangal, Telangana, India
| | - Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology Warangal, Telangana, India
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41
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Saha T, Sinha S, Harfoot R, Quiñones-Mateu ME, Das SC. Spray-Dried Inhalable Microparticles Combining Remdesivir and Ebselen against SARS-CoV-2 Infection. Pharmaceutics 2023; 15:2229. [PMID: 37765198 PMCID: PMC10535576 DOI: 10.3390/pharmaceutics15092229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
There is a continuous effort to develop efficient treatments for coronavirus disease 2019 (COVID-19) and other viral respiratory diseases. Among the different strategies, inhaled treatment is considered one of the most logical and efficient approaches to treating COVID-19, as the causative "SARS-CoV-2 virus RNA" predominantly infects the respiratory tract. COVID-19 treatments initially relied on repurposed drugs, with a few additional strategies developed during the last two years, and all of them are based on monotherapy. However, drug combinations have been found to be more effective than monotherapy in other viral diseases such as HIV, influenza, and hepatitis C virus. In the case of SARS-CoV-2 infection, in vitro studies have shown synergistic antiviral activity combining remdesivir with ebselen, an organoselenium compound. Therefore, these drug combinations could ensure better therapeutic outcomes than the individual agents. In this study, we developed a dry powder formulation containing remdesivir and ebselen using a spray-drying technique and used L-leucine as an aerosolization enhancer. The prepared dry powders were spherical and crystalline, with a mean particle size between 1 and 3 µm, indicating their suitability for inhalation. The emitted dose (ED) and fine particle fraction (FPF) of remdesivir- and ebselen-containing dry powders were ~80% and ~57% when prepared without L-leucine. The ED as well as the FPF significantly increased with values of >86% and >67%, respectively, when L-leucine was incorporated. More importantly, the single and combinational dry powder of remdesivir and ebselen showed minimal cytotoxicity (CC50 > 100 μM) in Calu-3 cells, retaining their anti-SARS-CoV-2 properties (EC50 2.77 to 18.64 μM). In summary, we developed an inhalable dry powder combination of remdesivir and ebselen using a spray-drying technique. The spray-dried inhalable microparticles retained their limited cytotoxicity and specific antiviral properties. Future in vivo studies are needed to verify the potential use of these remdesivir/ebselen combinational spray-dried inhalable microparticles to block the SARS-CoV-2 replication in the respiratory tract.
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Affiliation(s)
- Tushar Saha
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand;
| | - Shubhra Sinha
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; (S.S.); (R.H.); (M.E.Q.-M.)
| | - Rhodri Harfoot
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; (S.S.); (R.H.); (M.E.Q.-M.)
| | - Miguel E. Quiñones-Mateu
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; (S.S.); (R.H.); (M.E.Q.-M.)
| | - Shyamal C. Das
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand;
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42
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Hu Z, Liu Q, Ni Z. Facilitating the drug repurposing with iC/E strategy: A practice on novel nNOS inhibitor discovery. J Bioinform Comput Biol 2023; 21:2350018. [PMID: 37675491 DOI: 10.1142/s021972002350018x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Over the past decades, many existing drugs and clinical/preclinical compounds have been repositioned as new therapeutic indication from which they were originally intended and to treat off-target diseases by targeting their noncognate protein receptors, such as Sildenafil and Paxlovid, termed drug repurposing (DRP). Despite its significant attraction in the current medicinal community, the DRP is usually considered as a matter of accidents that cannot be fulfilled reliably by traditional drug discovery protocol. In this study, we proposed an integrated computational/experimental (iC/E) strategy to facilitate the DRP within a framework of rational drug design, which was practiced on the identification of new neuronal nitric oxide synthase (nNOS) inhibitors from a structurally diverse, functionally distinct drug pool. We demonstrated that the iC/E strategy is very efficient and readily feasible, which confirmed that the phosphodiesterase inhibitor DB06237 showed a high inhibitory potency against nNOS synthase domain, while other two general drugs, i.e. DB02302 and DB08258, can also inhibit the synthase at nanomolar level. Structural bioinformatics analysis revealed diverse noncovalent interactions such as hydrogen bonds, hydrophobic forces and van der Waals contacts across the complex interface of nNOS active site with these identified drugs, conferring both stability and specificity for the complex recognition and association.
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Affiliation(s)
- Zhaoyang Hu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Qingsen Liu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Zhong Ni
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, P. R. China
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Gurukkalot K, Rajendran V. Repurposing Polyether Ionophores as a New-Class of Anti-SARS-Cov-2 Agents as Adjunct Therapy. Curr Microbiol 2023; 80:273. [PMID: 37414909 DOI: 10.1007/s00284-023-03366-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
The emergence of SARS-CoV-2 and its variants have posed a significant threat to humankind in tackling the viral spread. Furthermore, currently repurposed drugs and frontline antiviral agents have failed to cure severe ongoing infections effectively. This insufficiency has fuelled research for potent and safe therapeutic agents to treat COVID-19. Nonetheless, various vaccine candidates have displayed a differential efficacy and need for repetitive dosing. The FDA-approved polyether ionophore veterinary antibiotic for treating coccidiosis has been repurposed for treating SARS-CoV-2 infection (as shown by both in vitro and in vivo studies) and other deadly human viruses. Based on selectivity index values, ionophores display therapeutic effects at sub-nanomolar concentrations and exhibit selective killing ability. They act on different viral targets (structural and non-structural proteins), host-cell components leading to SARS-CoV-2 inhibition, and their activity is further enhanced by Zn2+ supplementation. This review summarizes the anti-SARS-CoV-2 potential and molecular viral targets of selective ionophores like monensin, salinomycin, maduramicin, CP-80,219, nanchangmycin, narasin, X-206 and valinomycin. Ionophore combinations with Zn2+ are a new therapeutic strategy that warrants further investigation for possible human benefits.
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Affiliation(s)
- Keerthana Gurukkalot
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
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Bolz SN, Schroeder M. Promiscuity in drug discovery on the verge of the structural revolution: recent advances and future chances. Expert Opin Drug Discov 2023; 18:973-985. [PMID: 37489516 DOI: 10.1080/17460441.2023.2239700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
INTRODUCTION Promiscuity denotes the ability of ligands and targets to specifically interact with multiple binding partners. Despite negative aspects like side effects, promiscuity is receiving increasing attention in drug discovery as it can enhance drug efficacy and provides a molecular basis for drug repositioning. The three-dimensional structure of ligand-target complexes delivers exclusive insights into the molecular mechanisms of promiscuity and structure-based methods enable the identification of promiscuous interactions. With the recent breakthrough in protein structure prediction, novel possibilities open up to reveal unknown connections in ligand-target interaction networks. AREAS COVERED This review highlights the significance of structure in the identification and characterization of promiscuity and evaluates the potential of protein structure prediction to advance our knowledge of drug-target interaction networks. It discusses the definition and relevance of promiscuity in drug discovery and explores different approaches to detecting promiscuous ligands and targets. EXPERT OPINION Examination of structural data is essential for understanding and quantifying promiscuity. The recent advancements in structure prediction have resulted in an abundance of targets that are well-suited for structure-based methods like docking. In silico approaches may eventually completely transform our understanding of drug-target networks by complementing the millions of predicted protein structures with billions of predicted drug-target interactions.
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Affiliation(s)
- Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Dresden, Germany
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45
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Kumar S, Basu M, Ghosh P, Pal U, Ghosh MK. COVID-19 therapeutics: Clinical application of repurposed drugs and futuristic strategies for target-based drug discovery. Genes Dis 2023; 10:1402-1428. [PMID: 37334160 PMCID: PMC10079314 DOI: 10.1016/j.gendis.2022.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the complicated disease COVID-19. Clinicians are continuously facing huge problems in the treatment of patients, as COVID-19-specific drugs are not available, hence the principle of drug repurposing serves as a one-and-only hope. Globally, the repurposing of many drugs is underway; few of them are already approved by the regulatory bodies for their clinical use and most of them are in different phases of clinical trials. Here in this review, our main aim is to discuss in detail the up-to-date information on the target-based pharmacological classification of repurposed drugs, the potential mechanism of actions, and the current clinical trial status of various drugs which are under repurposing since early 2020. At last, we briefly proposed the probable pharmacological and therapeutic drug targets that may be preferred as a futuristic drug discovery approach in the development of effective medicines.
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Affiliation(s)
- Sunny Kumar
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector–V, Salt Lake, Kolkata-700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Malini Basu
- Department of Microbiology, Dhruba Chand Halder College, Dakshin Barasat, West Bengal 743372, India
| | - Pratyasha Ghosh
- Department of Economics, Bethune College, University of Calcutta, Kolkata 700006, India
| | - Uttam Pal
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector–V, Salt Lake, Kolkata-700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Mrinal K. Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector–V, Salt Lake, Kolkata-700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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Farid N, Bux K, Ali K, Bashir A, Tahir R. Repurposing Amphotericin B: anti-microbial, molecular docking and molecular dynamics simulation studies suggest inhibition potential of Amphotericin B against MRSA. BMC Chem 2023; 17:67. [PMID: 37386581 DOI: 10.1186/s13065-023-00980-9] [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: 04/14/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023] Open
Abstract
Amphotericin B (AMPH) is an anti-fungal drug and this study, for the first time as best of our knowledge, reports the repurposing of the Amphotericin B. The drug was found to show significant antibacterial potential revealed by antimicrobial screening, molecular docking, and mode of action analysis targeting Penicillin Binding Protein 2a (PBP 2a protein) which is target of β-lactam drugs and is involved in cell wall synthesis. Mode of action analysis showed the drug to have hydrophobic and hydrophilic interactions with both C-terminal, trans-peptidase and non-penicillin binding domain of the protein. Additionally, to evaluate the impact of ligand binding on the protein's conformational dynamics, molecular dynamics (MD) simulations were used. Comparative Dynamical flexibility (RMSF) and Dynamics Cross Correlation (DCCM) followed by MD simulations revealed the complex formation significantly effecting structural dynamics of the enzyme significantly in the non-penicillin binding domain (327-668) and slightly in trans peptidase domain. Radius of gyration assessment further showed ligand binding also decreasing over all compactness of protein. Secondary structure analysis indicated the complex formation changing the conformational integrity in non-penicillin binding domain. Hydrogen bond analysis and MMPBSA, free energy of calculations followed by MD simulations, also complemented the antimicrobial and molecular docking revelations suggesting Amphotericin B to have substantial antibacterial potential.
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Affiliation(s)
- Neha Farid
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan.
| | - Khair Bux
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan.
| | - Kashif Ali
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
| | - Asma Bashir
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
| | - Rahima Tahir
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
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Srivathsa AV, Sadashivappa NM, Hegde AK, Radha S, Mahesh AR, Ammunje DN, Sen D, Theivendren P, Govindaraj S, Kunjiappan S, Pavadai P. A Review on Artificial Intelligence Approaches and Rational Approaches in Drug Discovery. Curr Pharm Des 2023; 29:1180-1192. [PMID: 37132148 DOI: 10.2174/1381612829666230428110542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 05/04/2023]
Abstract
Artificial intelligence (AI) speeds up the drug development process and reduces its time, as well as the cost which is of enormous importance in outbreaks such as COVID-19. It uses a set of machine learning algorithms that collects the available data from resources, categorises, processes and develops novel learning methodologies. Virtual screening is a successful application of AI, which is used in screening huge drug-like databases and filtering to a small number of compounds. The brain's thinking of AI is its neural networking which uses techniques such as Convoluted Neural Network (CNN), Recursive Neural Network (RNN) or Generative Adversial Neural Network (GANN). The application ranges from small molecule drug discovery to the development of vaccines. In the present review article, we discussed various techniques of drug design, structure and ligand-based, pharmacokinetics and toxicity prediction using AI. The rapid phase of discovery is the need of the hour and AI is a targeted approach to achieve this.
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Affiliation(s)
- Anjana Vidya Srivathsa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Nandini Markuli Sadashivappa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Apeksha Krishnamurthy Hegde
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Srimathi Radha
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, Faculty of Medicine and Health Sciences, SRM Institute of Science and Technology, Chengalpattu District, Kattankulathur, Tamil Nadu, 603203, India
| | - Agasa Ramu Mahesh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Damodar Nayak Ammunje
- Department of Pharmacology, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
| | - Debanjan Sen
- Department of Pharmaceutical Chemistry, BCDA College of Pharmacy & Technology, Hridaypur, Kolkata, 700127, West Bengal, India
| | - Panneerselvam Theivendren
- Department of Pharmaceutical Chemistry, Swamy Vivekanandha College of Pharmacy, Elayampalayam, Tiruchengode, 637205, India
| | - Saravanan Govindaraj
- Department of Pharmaceutical Chemistry, MNR College of Pharmacy, Fasalwadi, Sangareddy, 502 001, India
| | - Selvaraj Kunjiappan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M.S.R. Nagar, Bengaluru, 560054, India
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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: 7] [Impact Index Per Article: 7.0] [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.
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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.
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Yang R, Liu L, Jiang D, Liu L, Yang H, Xu H, Qin M, Wang P, Gu J, Xing Y. Identification of Potential TMPRSS2 Inhibitors for COVID-19 Treatment in Chinese Medicine by Computational Approaches and Surface Plasmon Resonance Technology. J Chem Inf Model 2023; 63:3005-3017. [PMID: 37155923 DOI: 10.1021/acs.jcim.2c01643] [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: 05/10/2023]
Abstract
BACKGROUND Coronavirus disease-19 (COVID-19) pneumonia continues to spread in the entire globe with limited medication available. In this study, the active compounds in Chinese medicine (CM) recipes targeting the transmembrane serine protease 2 (TMPRSS2) protein for the treatment of COVID-19 were explored. METHODS The conformational structure of TMPRSS2 protein (TMPS2) was built through homology modeling. A training set covering TMPS2 inhibitors and decoy molecules was docked to TMPS2, and their docking poses were re-scored with scoring schemes. A receiver operating characteristic (ROC) curve was applied to select the best scoring function. Virtual screening of the candidate compounds (CCDs) in the six highly effective CM recipes against TMPS2 was conducted based on the validated docking protocol. The potential CCDs after docking were subject to molecular dynamics (MD) simulations and surface plasmon resonance (SPR) experiment. RESULTS A training set of 65 molecules were docked with modeled TMPS2 and LigScore2 with the highest area under the curve, AUC, value (0.886) after ROC analysis selected to best differentiate inhibitors from decoys. A total of 421 CCDs in the six recipes were successfully docked into TMPS2, and the top 16 CCDs with LigScore2 higher than the cutoff (4.995) were screened out. MD simulations revealed a stable binding between these CCDs and TMPS2 due to the negative binding free energy. Lastly, SPR experiments validated the direct combination of narirutin, saikosaponin B1, and rutin with TMPS2. CONCLUSIONS Specific active compounds including narirutin, saikosaponin B1, and rutin in CM recipes potentially target and inhibit TMPS2, probably exerting a therapeutic effect on COVID-19.
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Affiliation(s)
- Rong Yang
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Linhua Liu
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China
| | - Dansheng Jiang
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China
| | - Lei Liu
- Department of Infectious Diseases, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen 518033, China
| | - Huili Yang
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China
| | - Hongling Xu
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China
| | - Meirong Qin
- National Medical Products Administration, Shenzhen Institute for Drug Control, Shenzhen 518057, China
| | - Ping Wang
- National Medical Products Administration, Shenzhen Institute for Drug Control, Shenzhen 518057, China
| | - Jiangyong Gu
- Research Centre for Integrative Medicine, School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yufeng Xing
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, China
- Faculty of Chinese Medicine and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
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Hausdorff M, Delpal A, Barelier S, Nicollet L, Canard B, Touret F, Colmant A, Coutard B, Vasseur JJ, Decroly E, Debart F. Structure-guided optimization of adenosine mimetics as selective and potent inhibitors of coronavirus nsp14 N7-methyltransferases. Eur J Med Chem 2023; 256:115474. [PMID: 37192550 DOI: 10.1016/j.ejmech.2023.115474] [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: 02/16/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic reveals the urgent need to develop new therapeutics targeting the SARS-CoV-2 replication machinery. The first antiviral drugs were nucleoside analogues targeting RdRp and protease inhibitors active on nsp5 Mpro. In addition to these common antiviral targets, SARS-CoV-2 codes for the highly conserved protein nsp14 harbouring N7-methyltransferase (MTase) activity. Nsp14 is involved in cap N7-methylation of viral RNA and its inhibition impairs viral RNA translation and immune evasion, making it an attractive new antiviral target. In this work, we followed a structure-guided drug design approach to design bisubstrates mimicking the S-adenosylmethionine methyl donor and RNA cap. We developed adenosine mimetics with an N-arylsulfonamide moiety in the 5'-position, recently described as a guanine mimicking the cap structure in a potent adenosine-derived nsp14 inhibitor. Here, the adenine moiety was replaced by hypoxanthine, N6-methyladenine, or C7-substituted 7-deaza-adenine. 26 novel adenosine mimetics were synthesized, one of which selectively inhibits nsp14 N7-MTase activity with a subnanomolar IC50 (and seven with a single-digit nanomolar IC50). In the most potent inhibitors, adenine was replaced by two different 7-deaza-adenines bearing either a phenyl or a 3-quinoline group at the C7-position via an ethynyl linker. These more complex compounds are barely active on the cognate human N7-MTase and docking experiments reveal that their selectivity of inhibition might result from the positioning of their C7 substitution in a SAM entry tunnel present in the nsp14 structure and absent in the hN7-MTase. These compounds show moderate antiviral activity against SARS-CoV-2 replication in cell culture, suggesting delivery or stability issue.
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Affiliation(s)
- Marcel Hausdorff
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Adrien Delpal
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Sarah Barelier
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Laura Nicollet
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Franck Touret
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | - Agathe Colmant
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | - Bruno Coutard
- IHU Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, 13005, Marseille, France
| | | | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France.
| | - Françoise Debart
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France.
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