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Article ; Online: Artificial intelligence-driven drug repurposing and structural biology for SARS-CoV-2.

Prasad, Kartikay / Kumar, Vijay

Current research in pharmacology and drug discovery

2021 Volume 2, Page(s) 100042

Abstract: It has been said that COVID-19 is a generational challenge in many ways. But, at the same time, it becomes a catalyst for collective action, innovation, and discovery. Realizing the full potential of artificial intelligence (AI) for structure ... ...

Abstract	It has been said that COVID-19 is a generational challenge in many ways. But, at the same time, it becomes a catalyst for collective action, innovation, and discovery. Realizing the full potential of artificial intelligence (AI) for structure determination of unknown proteins and drug discovery are some of these innovations. Potential applications of AI include predicting the structure of the infectious proteins, identifying drugs that may be effective in targeting these proteins, and proposing new chemical compounds for further testing as potential drugs. AI and machine learning (ML) allow for rapid drug development including repurposing existing drugs. Algorithms were used to search for novel or approved antiviral drugs capable of inhibiting SARS-CoV-2. This paper presents a survey of AI and ML methods being used in various biochemistry of SARS-CoV-2, from structure to drug development, in the fight against the deadly COVID-19 pandemic. It is envisioned that this study will provide AI/ML researchers and the wider community an overview of the current status of AI applications particularly in structural biology, drug repurposing, and development, and motivate researchers in harnessing AI potentials in the fight against COVID-19.
Language	English
Publishing date	2021-07-28
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	2590-2571
ISSN (online)	2590-2571
DOI	10.1016/j.crphar.2021.100042
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Article ; Online: The SARS-CoV-2 targeted human RNA binding proteins network biology to investigate COVID-19 associated manifestations.

Prasad, Kartikay / Gour, Pratibha / Raghuvanshi, Saurabh / Kumar, Vijay

International journal of biological macromolecules

2022 Volume 217, Page(s) 853–863

Abstract: The global coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has had unprecedented social and economic ramifications. Identifying targets for drug repurposing could be an effective means to present new and fast treatments. ... ...

Abstract	The global coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has had unprecedented social and economic ramifications. Identifying targets for drug repurposing could be an effective means to present new and fast treatments. Furthermore, the risk of morbidity and mortality from COVID-19 goes up when there are coexisting medical conditions, however, the underlying mechanisms remain unclear. In the current study, we have adopted a network-based systems biology approach to investigate the RNA binding proteins (RBPs)-based molecular interplay between COVID-19, various human cancers, and neurological disorders. The network based on RBPs commonly involved in the three disease conditions consisted of nine RBPs connecting 10 different cancer types, 22 brain disorders, and COVID-19 infection, ultimately hinting at the comorbidities and complexity of COVID-19. Further, we underscored five miRNAs with reported antiviral properties that target all of the nine shared RBPs and are thus therapeutically valuable. As a strategy to improve the clinical conditions in comorbidities associated with COVID-19, we propose perturbing the shared RBPs by drug repurposing. The network-based analysis presented hereby contributes to a better knowledge of the molecular underpinnings of the comorbidities associated with COVID-19.
MeSH term(s)	Antiviral Agents/therapeutic use ; Biology ; Carrier Proteins ; Drug Repositioning ; Humans ; RNA-Binding Proteins/metabolism ; SARS-CoV-2 ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Carrier Proteins ; RNA-Binding Proteins
Language	English
Publishing date	2022-07-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2022.07.200
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Article: The SARS-CoV-2 targeted human RNA binding proteins network biology to investigate COVID-19 associated manifestations

Prasad, Kartikay / Gour, Pratibha / Raghuvanshi, Saurabh / Kumar, Vijay

International journal of biological macromolecules. 2022 Sept. 30, v. 217

2022

Abstract	The global coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has had unprecedented social and economic ramifications. Identifying targets for drug repurposing could be an effective means to present new and fast treatments. Furthermore, the risk of morbidity and mortality from COVID-19 goes up when there are coexisting medical conditions, however, the underlying mechanisms remain unclear. In the current study, we have adopted a network-based systems biology approach to investigate the RNA binding proteins (RBPs)-based molecular interplay between COVID-19, various human cancers, and neurological disorders. The network based on RBPs commonly involved in the three disease conditions consisted of nine RBPs connecting 10 different cancer types, 22 brain disorders, and COVID-19 infection, ultimately hinting at the comorbidities and complexity of COVID-19. Further, we underscored five miRNAs with reported antiviral properties that target all of the nine shared RBPs and are thus therapeutically valuable. As a strategy to improve the clinical conditions in comorbidities associated with COVID-19, we propose perturbing the shared RBPs by drug repurposing. The network-based analysis presented hereby contributes to a better knowledge of the molecular underpinnings of the comorbidities associated with COVID-19.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; brain ; drugs ; humans ; microRNA ; morbidity ; mortality ; pandemic ; risk ; viruses
Language	English
Dates of publication	2022-0930
Size	p. 853-863.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2022.07.200
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Article: Targeting cathepsins: A potential link between COVID-19 and associated neurological manifestations.

Prasad, Kartikay / Ahamad, Shahzaib / Gupta, Dinesh / Kumar, Vijay

Heliyon

2021 Volume 7, Issue 10, Page(s) e08089

Abstract: Many studies have shown that the lysosomal cathepsins, especially cathepsins B/L (CTSB/L) are required for SARS-CoV-2 entry into host cells. Lysosomal proteases, cathepsins are indispensable for normal health and are involved in several brain disorders ... ...

Abstract	Many studies have shown that the lysosomal cathepsins, especially cathepsins B/L (CTSB/L) are required for SARS-CoV-2 entry into host cells. Lysosomal proteases, cathepsins are indispensable for normal health and are involved in several brain disorders occurring at different development age periods. On the other hand, it has been well known that COVID-19 infection is largely associated with several neurological disorders. Taken together these findings and given the high levels of expression of CTSB/L in the brain, we here proposed a reasonable hypothesis about the involvement of CTSB/L in the neurological manifestations linked to COVID-19. Pharmacological inhibitions of the CTSB/L could be a potential therapeutic target to block the virus entry as well as to mitigate the brain disorders. To this end, we utilized the network-based drug repurposing analyses to identify the possible drugs that can target CTSB/L. This study identifies the molecules like cyclosporine, phenytoin, and paclitaxel as potential drugs with binding ability to the CTSB/L. Further, we have performed molecular docking and all-atom molecular dynamics (MD) simulations to investigate the stability of CTSL-drug complexes. The results showed strong and stable binding of drugs with CTSL.
Language	English
Publishing date	2021-09-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e08089
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Article ; Online: COVID-19 associated nervous system manifestations.

Khatoon, Fatima / Prasad, Kartikay / Kumar, Vijay

Sleep medicine

2021 Volume 91, Page(s) 231–236

Abstract: The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic in the last year. Along with major respiratory distress, a myriad of neurological manifestations was also ... ...

Abstract	The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic in the last year. Along with major respiratory distress, a myriad of neurological manifestations was also reported to be associated with COVID-19 patients. These cases indicate that SARS-CoV-2 can be considered as an opportunistic pathogen of the brain. SARS-CoV-2 enters the brain through the olfactory bulb, retrograde axonal transport from peripheral nerve endings, or via hematogenous or lymphatic routes. Notably, COVID-19 infection can cause or even present with different neurological features including encephalopathy, impaired consciousness, confusion, agitation, seizure, ataxia, headache, anosmia, ageusia, neuropathies, and neurodegenerative diseases. In this paper, we provide a brief review of observed neurological manifestations associated with COVID-19.
MeSH term(s)	Brain ; COVID-19/complications ; Humans ; Pandemics ; SARS-CoV-2 ; Seizures
Language	English
Publishing date	2021-07-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2012041-2
ISSN	1878-5506 ; 1389-9457
ISSN (online)	1878-5506
ISSN	1389-9457
DOI	10.1016/j.sleep.2021.07.005
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Article ; Online: Targeting cathepsins

Kartikay Prasad / Shahzaib Ahamad / Dinesh Gupta / Vijay Kumar

Heliyon, Vol 7, Iss 10, Pp e08089- (2021)

A potential link between COVID-19 and associated neurological manifestations

2021

Abstract	Many studies have shown that the lysosomal cathepsins, especially cathepsins B/L (CTSB/L) are required for SARS-CoV-2 entry into host cells. Lysosomal proteases, cathepsins are indispensable for normal health and are involved in several brain disorders occurring at different development age periods. On the other hand, it has been well known that COVID-19 infection is largely associated with several neurological disorders. Taken together these findings and given the high levels of expression of CTSB/L in the brain, we here proposed a reasonable hypothesis about the involvement of CTSB/L in the neurological manifestations linked to COVID-19. Pharmacological inhibitions of the CTSB/L could be a potential therapeutic target to block the virus entry as well as to mitigate the brain disorders. To this end, we utilized the network-based drug repurposing analyses to identify the possible drugs that can target CTSB/L. This study identifies the molecules like cyclosporine, phenytoin, and paclitaxel as potential drugs with binding ability to the CTSB/L. Further, we have performed molecular docking and all-atom molecular dynamics (MD) simulations to investigate the stability of CTSL-drug complexes. The results showed strong and stable binding of drugs with CTSL.
Keywords	COVID-19 ; SARS-CoV-2 ; Cathepsins ; Neurological manifestations ; Drug repurposing ; Cyclosporine ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	616
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Targeting cathepsins: A potential link between COVID-19 and associated neurological manifestations

Prasad, Kartikay / Ahamad, Shahzaib / Gupta, Dinesh / Kumar, Vijay

Heliyon. 2021 Oct., v. 7, no. 10

2021

Abstract	Many studies have shown that the lysosomal cathepsins, especially cathepsins B/L (CTSB/L) are required for SARS-CoV-2 entry into host cells. Lysosomal proteases, cathepsins are indispensable for normal health and are involved in several brain disorders occurring at different development age periods. On the other hand, it has been well known that COVID-19 infection is largely associated with several neurological disorders. Taken together these findings and given the high levels of expression of CTSB/L in the brain, we here proposed a reasonable hypothesis about the involvement of CTSB/L in the neurological manifestations linked to COVID-19. Pharmacological inhibitions of the CTSB/L could be a potential therapeutic target to block the virus entry as well as to mitigate the brain disorders. To this end, we utilized the network-based drug repurposing analyses to identify the possible drugs that can target CTSB/L. This study identifies the molecules like cyclosporine, phenytoin, and paclitaxel as potential drugs with binding ability to the CTSB/L. Further, we have performed molecular docking and all-atom molecular dynamics (MD) simulations to investigate the stability of CTSL-drug complexes. The results showed strong and stable binding of drugs with CTSL.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; brain ; cathepsins ; cyclosporine ; molecular dynamics ; paclitaxel ; phenytoin ; therapeutics ; viruses
Language	English
Dates of publication	2021-10
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e08089
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Article ; Online: Simultaneous Inhibition of SARS-CoV-2 Entry Pathways by Cyclosporine.

Prasad, Kartikay / Ahamad, Shahzaib / Kanipakam, Hema / Gupta, Dinesh / Kumar, Vijay

ACS chemical neuroscience

2021 Volume 12, Issue 5, Page(s) 930–944

Abstract: The COVID-19 pandemic caused by SARS-CoV-2 represents a global public health emergency. The entry of SARS-CoV-2 into host cells requires the activation of its spike protein by host cell proteases. The serine protease, TMPRSS2, and cysteine proteases, ... ...

Abstract	The COVID-19 pandemic caused by SARS-CoV-2 represents a global public health emergency. The entry of SARS-CoV-2 into host cells requires the activation of its spike protein by host cell proteases. The serine protease, TMPRSS2, and cysteine proteases, Cathepsins B/L, activate spike protein and enable SARS-CoV-2 entry to the host cell through two completely different and independent pathways. Therefore, inhibiting either TMPRSS2 or cathepsin B/L may not sufficiently block the virus entry. We here hypothesized that simultaneous targeting of both the entry pathways would be more efficient to block the virus entry rather than targeting the entry pathways individually. To this end, we utilized the network-based drug repurposing analyses to identify the possible common drugs that can target both the entry pathways. This study, for the first time, reports the molecules like cyclosporine, calcitriol, and estradiol as candidate drugs with the binding ability to the host proteases, TMPRSS2, and cathepsin B/L. Next, we analyzed drug-gene and gene-gene interaction networks using 332 human targets of SARS-CoV-2 proteins. The network results indicate that, out of 332 human proteins, cyclosporine interacts with 216 (65%) proteins. Furthermore, we performed molecular docking and all-atom molecular dynamics (MD) simulations to explore the binding of drug with TMPRSS2 and cathepsin L. The molecular docking and MD simulation results showed strong and stable binding of cyclosporine A (CsA) with TMPRSS2 and CTSL genes. The above results indicate cyclosporine as a potential drug molecule, as apart from interacting with SARS-CoV-2 entry receptors, it also interacts with most of SARS-CoV-2 target host genes; thus it could potentially interfere with functions of SARS-CoV-2 proteins in human cells. We here also suggest that these antiviral drugs alone or in combination can simultaneously target both the entry pathways and thus can be considered as a potential treatment option for COVID-19.
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19/virology ; Cathepsin B/metabolism ; Cathepsin L/metabolism ; Cyclosporine/pharmacology ; Drug Repositioning ; Humans ; Immunosuppressive Agents/pharmacology ; Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Pandemics ; SARS-CoV-2/drug effects ; Serine Endopeptidases/metabolism ; Virus Internalization/drug effects
Chemical Substances	Antiviral Agents ; Immunosuppressive Agents ; Cyclosporine (83HN0GTJ6D) ; Serine Endopeptidases (EC 3.4.21.-) ; TMPRSS2 protein, human (EC 3.4.21.-) ; Cathepsin B (EC 3.4.22.1) ; Cathepsin L (EC 3.4.22.15)
Language	English
Publishing date	2021-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.1c00019
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Article ; Online: Neurological manifestations of COVID-19: available evidences and a new paradigm.

Khatoon, Fatima / Prasad, Kartikay / Kumar, Vijay

Journal of neurovirology

2020 Volume 26, Issue 5, Page(s) 619–630

Abstract: The recent pandemic outbreak of coronavirus is pathogenic and a highly transmittable viral infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2). In this time of ongoing pandemic, many emerging reports suggested that the SARS- ... ...

Abstract	The recent pandemic outbreak of coronavirus is pathogenic and a highly transmittable viral infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2). In this time of ongoing pandemic, many emerging reports suggested that the SARS-CoV-2 has inimical effects on neurological functions, and even causes serious neurological damage. The neurological symptoms associated with COVID-19 include headache, dizziness, depression, anosmia, encephalitis, stroke, epileptic seizures, and Guillain-Barre syndrome along with many others. The involvement of the CNS may be related with poor prognosis and disease worsening. Here, we review the evidence of nervous system involvement and currently known neurological manifestations in COVID-19 infections caused by SARS-CoV-2. We prioritize the 332 human targets of SARS-CoV-2 according to their association with brain-related disease and identified 73 candidate genes. We prioritize these 73 genes according to their spatio-temporal expression in the different regions of brain and also through evolutionary intolerance analysis. The prioritized genes could be considered potential indicators of COVID-19-associated neurological symptoms and thus act as a possible therapeutic target for the prevention and treatment of CNS manifestations associated with COVID-19 patients.
MeSH term(s)	Betacoronavirus/pathogenicity ; Brain/metabolism ; Brain/pathology ; Brain/virology ; COVID-19 ; Coronavirus Infections/complications ; Coronavirus Infections/genetics ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Depression ; Dizziness/complications ; Dizziness/genetics ; Dizziness/pathology ; Dizziness/virology ; Encephalitis/complications ; Encephalitis/genetics ; Encephalitis/pathology ; Encephalitis/virology ; Guillain-Barre Syndrome/complications ; Guillain-Barre Syndrome/genetics ; Guillain-Barre Syndrome/pathology ; Guillain-Barre Syndrome/virology ; Headache/complications ; Headache/genetics ; Headache/pathology ; Headache/virology ; Host-Pathogen Interactions/genetics ; Humans ; Nerve Tissue Proteins/classification ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Olfaction Disorders/complications ; Olfaction Disorders/genetics ; Olfaction Disorders/pathology ; Olfaction Disorders/virology ; Pandemics ; Pneumonia, Viral/complications ; Pneumonia, Viral/genetics ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; Protein Interaction Mapping ; SARS-CoV-2 ; Seizures/complications ; Seizures/genetics ; Seizures/pathology ; Seizures/virology ; Severity of Illness Index ; Stroke/complications ; Stroke/genetics ; Stroke/pathology ; Stroke/virology ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Nerve Tissue Proteins ; Viral Proteins
Keywords	covid19
Language	English
Publishing date	2020-08-24
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1283265-0
ISSN	1538-2443 ; 1355-0284
ISSN (online)	1538-2443
ISSN	1355-0284
DOI	10.1007/s13365-020-00895-4
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Article ; Online: Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis.

Pandey, Preeti / Prasad, Kartikay / Prakash, Amresh / Kumar, Vijay

Journal of molecular medicine (Berlin, Germany)

2020 Volume 98, Issue 12, Page(s) 1659–1673

Abstract: The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus continually led to infect a large population worldwide. SARS-CoV-2 utilizes its NSP6 and Orf9c proteins to interact ... ...

Abstract	The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus continually led to infect a large population worldwide. SARS-CoV-2 utilizes its NSP6 and Orf9c proteins to interact with sigma receptors that are implicated in lipid remodeling and ER stress response, to infect cells. The drugs targeting the sigma receptors, sigma-1 and sigma-2, have emerged as effective candidates to reduce viral infectivity, and some of them are in clinical trials against COVID-19. The antipsychotic drug, haloperidol, exerts remarkable antiviral activity, but, at the same time, the sigma-1 benzomorphan agonist, dextromethorphan, showed pro-viral activity. To explore the potential mechanisms of biased binding and activity of the two drugs, haloperidol and dextromethorphan towards NSP6, we herein utilized molecular docking-based molecular dynamics simulation studies. Our extensive analysis of the protein-drug interactions, structural and conformational dynamics, residual frustrations, and molecular switches of NSP6-drug complexes indicates that dextromethorphan binding leads to structural destabilization and increase in conformational dynamics and energetic frustrations. On the other hand, the strong binding of haloperidol leads to minimal structural and dynamical perturbations to NSP6. Thus, the structural insights of stronger binding affinity and favorable molecular interactions of haloperidol towards viral NSP6 suggests that haloperidol can be potentially explored as a candidate drug against COVID-19. KEY MESSAGES: •Inhibitors of sigma receptors are considered as potent drugs against COVID-19. •Antipsychotic drug, haloperidol, binds strongly to NSP6 and induces the minimal changes in structure and dynamics of NSP6. •Dextromethorphan, agonist of sigma receptors, binding leads to overall destabilization of NSP6. •These two drugs bind with NSP6 differently and also induce differences in the structural and conformational changes that explain their different mechanisms of action. •Haloperidol can be explored as a candidate drug against COVID-19.
MeSH term(s)	Binding Sites/drug effects ; COVID-19/drug therapy ; COVID-19/virology ; Computer Simulation ; Coronavirus Nucleocapsid Proteins/chemistry ; Coronavirus Nucleocapsid Proteins/genetics ; Dextromethorphan/chemistry ; Dextromethorphan/therapeutic use ; Haloperidol/chemistry ; Haloperidol/therapeutic use ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Pandemics ; Protein Binding/drug effects ; Protein Interaction Domains and Motifs/drug effects ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity
Chemical Substances	Coronavirus Nucleocapsid Proteins ; NSP6 protein, SARS-CoV-2 ; Dextromethorphan (7355X3ROTS) ; Haloperidol (J6292F8L3D)
Keywords	covid19
Language	English
Publishing date	2020-09-23
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1223802-8
ISSN	1432-1440 ; 0946-2716
ISSN (online)	1432-1440
ISSN	0946-2716
DOI	10.1007/s00109-020-01980-1
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