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Kulandaisamy R, Kushwaha T, Dalal A, Kumar V, Singh D, Baswal K, Sharma P, Praneeth K, Jorwal P, Kayampeta SR, Sharma T, Maddur S, Kumar M, Kumar S, Polamarasetty A, Singh A, Sehgal D, Gholap SL, Appaiahgari MB, Katika MR, Inampudi KK. Repurposing of FDA Approved Drugs Against SARS-CoV-2 Papain-Like Protease: Computational, Biochemical, and in vitro Studies. Front Microbiol 2022; 13:877813. [PMID: 35620103 PMCID: PMC9127501 DOI: 10.3389/fmicb.2022.877813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
The pandemic caused by SARS-CoV-2 (SCoV-2) has impacted the world in many ways and the virus continues to evolve and produce novel variants with the ability to cause frequent global outbreaks. Although the advent of the vaccines abated the global burden, they were not effective against all the variants of SCoV-2. This trend warrants shifting the focus on the development of small molecules targeting the crucial proteins of the viral replication machinery as effective therapeutic solutions. The PLpro is a crucial enzyme having multiple roles during the viral life cycle and is a well-established drug target. In this study, we identified 12 potential inhibitors of PLpro through virtual screening of the FDA-approved drug library. Docking and molecular dynamics simulation studies suggested that these molecules bind to the PLpro through multiple interactions. Further, IC50 values obtained from enzyme-inhibition assays affirm the stronger affinities of the identified molecules for the PLpro. Also, we demonstrated high structural conservation in the catalytic site of PLpro between SCoV-2 and Human Coronavirus 229E (HCoV-229E) through molecular modelling studies. Based on these similarities in PLpro structures and the resemblance in various signalling pathways for the two viruses, we propose that HCoV-229E is a suitable surrogate for SCoV-2 in drug-discovery studies. Validating our hypothesis, Mefloquine, which was effective against HCoV-229E, was found to be effective against SCoV-2 as well in cell-based assays. Overall, the present study demonstrated Mefloquine as a potential inhibitor of SCoV-2 PLpro and its antiviral activity against SCoV-2. Corroborating our findings, based on the in vitro virus inhibition assays, a recent study reported a prophylactic role for Mefloquine against SCoV-2. Accordingly, Mefloquine may further be investigated for its potential as a drug candidate for the treatment of COVID.
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Affiliation(s)
| | - Tushar Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Anu Dalal
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi, India
| | - Vikas Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Deepa Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Kamal Baswal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Pratibha Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Kokkula Praneeth
- Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
| | - Pankaj Jorwal
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sarala R Kayampeta
- Research and Development Division, Srikara Biologicals Private Limited, Tirupati, India
| | - Tamanna Sharma
- Central Research Laboratory Mobile Virology Research and Development BSL3 Lab, Employees' State Insurance Corporation Medical College and Hospital, Hyderabad, India
| | - Srinivas Maddur
- Central Research Laboratory Mobile Virology Research and Development BSL3 Lab, Employees' State Insurance Corporation Medical College and Hospital, Hyderabad, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Aparoy Polamarasetty
- Faculty of Biology, Indian Institute of Petroleum and Energy, Visakhapatnam, India
| | - Aekagra Singh
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Deepak Sehgal
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Shivajirao L Gholap
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi, India
| | - Mohan B Appaiahgari
- Research and Development Division, Srikara Biologicals Private Limited, Tirupati, India
| | - Madhumohan R Katika
- Central Research Laboratory Mobile Virology Research and Development BSL3 Lab, Employees' State Insurance Corporation Medical College and Hospital, Hyderabad, India.,Stem Cell Facility and Regenerative Medicine, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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Saito H, Ebinuma H, Ojiro K, Wakabayashi K, Inoue M, Tada S, Hibi T. On-treatment predictions of success in peg-interferon/ribavirin treatment using a novel formula. World J Gastroenterol 2010; 16:89-97. [PMID: 20039454 PMCID: PMC2799922 DOI: 10.3748/wjg.v16.i1.89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To predict treatment success using only simple clinical data from peg-interferon plus ribavirin therapy for chronic hepatitis C.
METHODS: We analyzed the clinical data of 176 patients with chronic hepatitis and hepatitis C virus genotype 1 who received 48 wk standard therapy, derived a predictive formula to assess a sustained virological response of the individual patient using a logistic regression model and confirmed the validity of this formula. The formula was constructed using data from the first 100 patients enrolled and validated using data from the remaining 76 patients.
RESULTS: Sustained virological response was obtained in 83 (47.2%) of the patients and we derived formulae to predict sustained virological response at pretreatment and weeks 4, 12 and 24. The likelihood of sustained virological response could be predicted effectively by the formulae at weeks 4, 12 and 24 (the area under the curve of the receiver operating characteristic: 0.821, 0.802, and 0.891, respectively), but not at baseline (0.570). The formula at week 48 was also constructed and validation by test data achieved good prediction with 0.871 of the area under the curve of the receiver operating characteristic. Prediction by this formula was always superior to that by viral kinetics.
CONCLUSION: These results suggested that our formula combined with viral kinetics provides a clear direction of therapy for each patient and enables the best tailored treatment.
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Saito H, Tada S, Ebinuma H, Ishii H, Kashiwazaki K, Takahashi M, Tsukada N, Nishida J, Tanaka S, Shiozaki H, Hibi T. Role of erythrocytes as a reservoir for ribavirin and relationship with adverse reactions in the early phase of interferon combination therapy for chronic hepatitis C virus infections. J Clin Microbiol 2006; 44:3562-8. [PMID: 17021083 PMCID: PMC1594781 DOI: 10.1128/jcm.00079-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We investigated the relationship between serum ribavirin concentrations and clearance, as well as therapeutic efficacy and adverse reactions, in 97 Japanese patients with chronic hepatitis C virus infections treated with a 6-month course of high-dose alpha2b interferon (6 million units/day) plus ribavirin (600 to 800 mg/day) combination therapy. This randomized trial showed that the saturation of ribavirin uptake after taking ribavirin capsules does not occur within a dose range of 600 to 800 mg/day, which is a standard dosage used clinically in Japan. Serum ribavirin concentrations and clearance did not correlate with sustained virological response rates. Fourteen patients discontinued therapy because of adverse reactions, and sustained virological response rates were significantly reduced by discontinuation of therapy, while dose reduction of ribavirin did not alter the therapeutic effects. Ribavirin concentrations after 1 week and ribavirin clearance were significantly correlated with discontinuation of ribavirin; however, a multiple-regression analysis revealed that only hemoglobin concentration, but not ribavirin clearance, was a significant factor for discontinuation of therapy (odds ratio, 0.514; 95% confidence interval, 0.311 to 0.85; P = 0.0095). It appears that peripheral erythrocytes may act as a reservoir for ribavirin and regulate serum ribavirin levels in the very early phase of treatment.
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Affiliation(s)
- Hidetsugu Saito
- Department of Internal Medicine, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
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Miyaguchi S, Saito H, Ebinuma H, Morizane T, Ishii H. Possible association between HLA antigens and the response to interferon in Japanese patients with chronic hepatitis C. TISSUE ANTIGENS 1997; 49:605-11. [PMID: 9234482 DOI: 10.1111/j.1399-0039.1997.tb02808.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Correlation between the major histocompatibility complex class I antigens (HLA-A, -B and -C) and the elimination from serum of hepatitis C virus in patients with chronic hepatitis C has not been understood. We analyzed HLA phenotypes and their relationship to the efficacy of interferon treatment. Of the 172 patients who were treated with 9 million units of interferon-alpha 2a three times a week for 6 months, 54 patients were responders and 118 patients were non-responders. No significant difference was observed between the 172 patients and 199 healthy subjects with regard to the frequencies of HLA-A, -B and -C antigen phenotypes. However, HLA-B55, B62, CW3 and CW4 frequencies were significantly higher in responders than in non-responders to the interferon treatment. CW4 was found to link with B62, but other phenotypes were independent each other. Patients with HLA B55, B62 and CW3 had a significantly lower viral load, and showed a better response to interferon. These results suggest that HLA system does not have an influence on the evolution towards chronicity of the disease due to hepatitis C virus, but HLA B55, B62 or CW4, and CW3 may be a virus quantity-regulating factors which then affect to response to the interferon treatment, indicating that these HLA antigens in conjunction with a viral peptide is a key target antigen for cytotoxic T lymphocytes in patients with chronic hepatitis C.
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Affiliation(s)
- S Miyaguchi
- Department of Internal Medicine, Tokyo Metropolitan Otsuka Hospital, Japan
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