School Of Basic And Applied Sciences

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    Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis
    (MDPI, 2023-03-28T00:00:00) Kumar, Reetesh; Srivastava, Yogesh; Muthuramalingam, Pandiyan; Singh, Sunil Kumar; Verma, Geetika; Tiwari, Savitri; Tandel, Nikunj; Beura, Samir Kumar; Panigrahi, Abhishek Ramachandra; Maji, Somnath; Sharma, Prakriti; Rai, Pankaj Kumar; Prajapati, Dinesh Kumar; Shin, Hyunsuk; Tyagi, Rajeev K.
    Genetic variant(s) of concern (VoC) of SARS-CoV-2 have been emerging worldwide due to mutations in the gene encoding spike glycoprotein. We performed comprehensive analyses of spike protein mutations in the significant variant clade of SARS-CoV-2, using the data available on the Nextstrain server. We selected various mutations, namely, A222V, N439K, N501Y, L452R, Y453F, E484K, K417N, T478K, L981F, L212I, N856K, T547K, G496S, and Y369C for this study. These mutations were chosen based on their global entropic score, emergence, spread, transmission, and their location in the spike receptor binding domain (RBD). The relative abundance of these mutations was mapped with global mutation D614G as a reference. Our analyses suggest the rapid emergence of newer global mutations alongside D614G, as reported during the recent waves of COVID-19 in various parts of the world. These mutations could be instrumentally imperative for the transmission, infectivity, virulence, and host immune system�s evasion of SARS-CoV-2. The probable impact of these mutations on vaccine effectiveness, antigenic diversity, antibody interactions, protein stability, RBD flexibility, and accessibility to human cell receptor ACE2 was studied in silico. Overall, the present study can help researchers to design the next generation of vaccines and biotherapeutics to combat COVID-19 infection. � 2023 by the authors.
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    Insights into the Scenario of SARS-CoV-2 Infection in Male Reproductive Toxicity
    (MDPI, 2023-02-23T00:00:00) Mukherjee, Anirban Goutam; Wanjari, Uddesh Ramesh; Gopalakrishnan, Abilash Valsala; Kannampuzha, Sandra; Murali, Reshma; Namachivayam, Arunraj; Ganesan, Raja; Renu, Kaviyarasi; Dey, Abhijit; Vellingiri, Balachandar; Prabakaran, D.S.
    COVID-19 has become a significant public health concern that has catastrophic consequences for society. Some preliminary evidence suggests that the male reproductive system may be an infection target for SARS-CoV-2. SARS-CoV-2 may be transmitted sexually, according to preliminary research. Testicular cells exhibit a high level of the angiotensin-converting enzyme 2 (ACE2) receptor, which enhances the entry of the SARS-CoV-2 into host cells. Some instances of COVID-19 have been documented to exhibit hypogonadism during the acute stage. Furthermore, systemic inflammatory reactions triggered by SARS-CoV-2 infection may cause oxidative stress (OS), which has been shown to have profoundly deleterious consequences on testicular functioning. This work gives a clear picture of how COVID-19 may affect male reproductive systems and calls attention to the many unanswered questions about the mechanisms by which this virus can be linked to men�s health and fertility. � 2023 by the authors.
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    Phytochemicals as Potential Therapeutics for SARS-CoV-2�Induced Cardiovascular Complications: Thrombosis and Platelet Perspective
    (Frontiers Media S.A., 2021-04-26T00:00:00) Beura, Samir K.; Panigrahi, Abhishek R.; Yadav, Pooja; Singh, Sunil K.
    After gaining entry through ACE2 aided by TMPRSS2, the SARS-CoV-2 causes serious complications of the cardiovascular system leading to myocarditis and other myocardial injuries apart from causing lung, kidney and brain dysfunctions. Here in this review, we are going to divulge the cellular and immunological mechanisms behind the cardiovascular, thrombotic and platelet impairments that are caused in COVID-19. In addition, we also propose the significance of various anti-platelet and anti-thrombotic phytochemicals in the treatment of COVID-19. The virus induces many immune-modulatory cytokines and chemokines which help in the intravascular coagulation and create a pro-thrombotic environment along with pulmonary embolism and thrombocytopenia. Different types of innate and adaptive immune cells and their granular contents regulate the pathophysiology of SARS-CoV-2 induced endothelial and platelet dysfunctions which correlate the involvement of platelets with myocardial injury and intravascular thrombi directly or indirectly. Hence, by exploiting the natural bioactive compounds from medicinal plants and inhibiting the platelet mediated thrombus formation can be beneficial for the treatment of SARS-CoV-2 infection. � Copyright � 2021 Beura, Panigrahi, Yadav and Singh.
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    Current Insights and Molecular Docking Studies of the Drugs under Clinical Trial as RdRp Inhibitors in COVID-19 Treatment
    (Bentham Science Publishers, 2022-11-08T00:00:00) Pauly, Irine; Singh, Ankit Kumar; Kumar, Adarsh; Singh, Yogesh; Thareja, Suresh; Kamal, Mohammad A.; Verma, Amita; Kumar, Pradeep
    Study Background & Objective: After the influenza pandemic (1918), COVID-19 was declared a Vth pandemic by the WHO in 2020. SARS-CoV-2 is an RNA-enveloped single-stranded virus. Based on the structure and life cycle, Protease (3CLpro), RdRp, ACE2, IL-6, and TMPRSS2 are the major targets for drug development against COVID-19. Pre-existing several drugs (FDA-approved) are used to inhibit the above targets in different diseases. In coronavirus treatment, these drugs are also in different clinical trial stages. Remdesivir (RdRp inhibitor) is the only FDA-approved medicine for coronavirus treatment. In the present study, by using the drug repurposing strategy, 70 preexisting clinical or under clinical trial molecules were used in scrutiny for RdRp inhibitor potent molecules in coronavirus treatment being surveyed via docking studies. Molecular simulation studies further confirmed the binding mechanism and stability of the most potent compounds. Material and Methods: Docking studies were performed using the Maestro 12.9 module of Schrodinger soft-ware over 70 molecules with RdRp as the target and remdesivir as the standard drug and further confirmed by simulation studies. Results: The docking studies showed that many HIV protease inhibitors demonstrated remarkable binding interactions with the target RdRp. Protease inhibitors such as lopinavir and ritonavir are effective. Along with these, AT-527, ledipasvir, bicalutamide, and cobicistat showed improved docking scores. RMSD and RMSF were further analyzed for potent ledipasvir and ritonavir by simulation studies and were identified as potential candidates for corona disease. Conclusion: The drug repurposing approach provides a new avenue in COVID-19 treatment. � 2022 Bentham Science Publishers.
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    Development of gold nanoparticle-based biosensors for COVID-19 diagnosis
    (Springer Science and Business Media Deutschland GmbH, 2022-09-05T00:00:00) Khan, Johra; Rasmi, Yousef; K?rbo?a, Kevser K�bra; Ali, Ahmad; Rudrapal, Mithun; Patekar, Rohan R.
    Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative organism of coronavirus disease 2019 (COVID-19) which poses a significant threat to public health worldwide. Though there are certain recommended drugs that can cure COVID-19, their therapeutic efficacy is limited. Therefore, the early and rapid detection without compromising the test accuracy is necessary in order to provide an appropriate treatment for the disease suppression. Main body: Nanoparticles (NPs) can closely mimic the virus and interact strongly with its proteins due to their morphological similarities. NPs have been widely applied in a variety of medical applications, including biosensing, drug delivery, antimicrobial treatment, and imaging. Recently, NPs-based biosensors have attracted great interest for their biological activities and specific sensing properties, which allows the detection of analytes such as nucleic acids (DNA or RNA), aptamers, and proteins in clinical samples. Further, the advances of nanotechnologies have enabled the development of miniaturized detection systems for point-of-care biosensors, a new strategy for detecting human viral diseases. Among the various NPs, the specific physicochemical properties of gold NPs (AuNPs) are being widely used in the field of clinical diagnostics. As a result, several AuNP-based colorimetric detection methods have been developed. Short conclusion: The purpose of this review is to provide an overview of the development of AuNPs-based biosensors by virtue of its powerful characteristics as a signal amplifier or enhancer that target pathogenic RNA viruses that provide a reliable and effective strategy for detecting of the existing or newly emerging SARS-CoV-2. � 2022, The Author(s).
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    Exploring the COVID-19 vaccine candidates against SARS-CoV-2 and its variants: where do we stand and where do we go?
    (Taylor and Francis Ltd., 2021-12-03T00:00:00) Joshi, Gaurav; Borah, Pobitra; Thakur, Shweta; Sharma, Praveen; Mayank; Poduri, Ramarao
    As of September 2021, 117 COVID-19 vaccines are in clinical development, and 194 are in preclinical development as per the World Health Organization (WHO) published draft landscape. Among the 117 vaccines undergoing clinical trials, the major platforms include protein subunit; RNA; inactivated virus; viral vector, among others. So far, USFDA recognized to approve the Pfizer-BioNTech (Comirnaty) COVID-19 vaccine for its full use in individuals of 16�years of age and older. Though the approved vaccines are being manufactured at a tremendous pace, the wealthiest countries have about 28% of total vaccines despite possessing only 10.8% of the total world population, suggesting an inequity of vaccine distribution. The review comprehensively summarizes the history of vaccines, mainly focusing on vaccines for SARS-CoV-2. The review also connects relevant topics, including measurement of vaccines efficacy against SARS-CoV-2 and its variants, associated challenges, and limitations, as hurdles in global vaccination are also kept forth. � 2021 Taylor & Francis Group, LLC.
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    Recent efforts for drug identification from phytochemicals against SARS-CoV-2: Exploration of the chemical space to identify druggable leads
    (Elsevier Ltd, 2021-04-03T00:00:00) Joshi, Gaurav; Sindhu, Jayant; Thakur, Shikha; Rana, Abhilash; Sharma, Geetika; Mayank; Poduri, Ramarao
    Nature, which remains a central drug discovery pool, is always looked upon to find a putative druggable lead. The natural products and phytochemical derived from plants are essential during a global health crisis. This class represents one of the most practical and promising approaches to decrease pandemic's intensity owing to their therapeutic potential. The present manuscript is therefore kept forth to give the researchers updated information on undergoing research in allied areas of natural product-based drug discovery, particularly for Covid-19 disease. The study briefly shreds evidence from in vitro and in silico researches done so far to find a lead molecule against Covid-19. Following this, we exhaustively explored the concept of chemical space and molecular similarity parameters for the drug discovery about the lead(s) generated from in silico-based studies. The comparison was drawn using FDA-approved anti-infective agents during 2015�2020 using key descriptors to evaluate druglike properties. The outcomes of results were further corroborated using Molecular Dynamics studies which suggested the outcomes in alignment with chemical space ranking. In a nutshell, current research work aims to provide a holistic strategic approach to drug design, keeping in view the identified phytochemicals against Covid-19. � 2021 Elsevier Ltd
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    Selection of active antiviral compounds against COVID-19 disease targeting coronavirus endoribonuclease nendou/NSP15 via ligand-based virtual screening and molecular docking
    (Bentham Science Publishers, 2020-12-15T00:00:00) Joshi, Gaurav; Poduri, Ramarao
    Background: The rapid spread of SARS-CoV-2 has caused havoc and panic among individuals, which has further worsened due to the unavailability of a proven drug(s) regime. Objective: The current work involves drug repurposing from the pool of USFDA approved drugs involving in silico virtual screening technique against COVID-19. Materials and Methods: Methodology involves virtual screening of 8548 FDA approved drugs against target protein endoribonuclease NendoU (Nsp15) (PDB ID: 6VWW). Result: Virtual screening-based analysis enabled us to identify four drugs, Eprosartan, Inarigivir soproxil, Foretinib, and DB01813 that could plausibly target Nsp15 against COVID-19 disease. Conclusion: The work offers the scope to corroborate the findings via in vitro and in vivo techniques to identify the potential of selected leads against COVID-19. The outcome may also help in tracing their molecular mechanism(s) in addition to their development at the clinical level in the future. � 2021 Bentham Science Publishers.
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    Exploring the magic bullets to identify Achilles� heel in SARS-CoV-2: Delving deeper into the sea of possible therapeutic options in Covid-19 disease: An update
    (Elsevier Ltd, 2020-11-27T00:00:00) Thakur, Shikha; Mayank; Sarkar, Bibekananda; Ansari, Arshad J.; Khandelwal, Akanksha; Arya, Anil; Poduri, Ramarao; Joshi, Gaurav
    The symptoms associated with Covid-19 caused by SARS-CoV-2 in severe conditions can cause multiple organ failure and fatality via a plethora of mechanisms, and it is essential to discover the efficacious and safe drug. For this, a successful strategy is to inhibit in different stages of the SARS-CoV-2 life cycle and host cell reactions. The current review briefly put forth the summary of the SARS-CoV-2 pandemic and highlight the critical areas of understanding in genomics, proteomics, medicinal chemistry, and natural products derived drug discovery. The review further extends to briefly put forth the updates in the drug testing system, biologics, biophysics, and their advances concerning SARS-CoV-2. The salient features include information on SARS-CoV-2 morphology, genomic characterization, and pathophysiology along with important protein targets and how they influence the drug design and development against SARS-CoV-2 and a concerted and integrated approach to target these stages. The review also gives the status of drug design and discovery to identify the drugs acting on critical targets in SARS-CoV-2 and host reactions to treat Covid-19. � 2020 Elsevier Ltd
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    Nanotechnology: Roles in diagnosis and treatment of covid-19
    (Collegium Basilea, 2021-10-11T00:00:00) Borgohain, Venus; Kumar, Vinay
    Nanotechnology has diverse applications in medical research including viral detection. The potential use of nanotechnology to detect SARS-CoV-2, and to treat and prevent Covid-19, is highlighted in this review. For detection, the isolation of total RNA and characterization using room-temperature loop-mediated isothermal amplification (RT-LAMP) looks promising. Preventive measures such as the development and delivery of vaccines can also be effectively carried out using nanotechnology, especially nanoparticles mediating the efficient delivery of vaccines and for delivering siRNA to specific target sites for silencing viral genes. Other aspects of nanotechnology can also be harnessed in the fight against SARS-CoV-2, including nanomaterials to enhance the efficiency of surgical masks and keep surfaces likely to receive viruses sterile. � 2021 Collegium Basilea.