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Article ; Online: Computational investigation on

Murugan, Natarajan Arul / Pandian, Chitra Jeyaraj / Jeyakanthan, Jeyaraman

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 12, Page(s) 4415–4426

Abstract: ... approach of drug development. This is only possible if we use reliable computational approaches ... for screening compounds from chemical space or by drug repurposing or by finding the phytochemicals and ... and Chinese medicine. Here using molecular docking approach, and combined molecular dynamics and MM ...

Abstract	The outbreak due to SARS-CoV-2 (or Covid-19) is spreading alarmingly and number of deaths due to infection is aggressively increasing every day. Due to the rapid human to human transmission of Covid-19, we are in need to find a potent drug at the earliest by ruling-out the traditional time-consuming approach of drug development. This is only possible if we use reliable computational approaches for screening compounds from chemical space or by drug repurposing or by finding the phytochemicals and nutraceuticals from plants as they can be immediately used without the need for carrying out drug-trials to test safety and efficacy. A number of plant products were routinely suggested as drugs in traditional Indian and Chinese medicine. Here using molecular docking approach, and combined molecular dynamics and MM-GBSA based free energy calculations approach, we study the potency of the four selected phytochemicals namely andrographolide (AGP1), 14-deoxy 11,12-didehydro andrographolide (AGP2), neoandrographolide (AGP3) and 14-deoxy andrographolide (AGP4) from
MeSH term(s)	Andrographis ; Antiviral Agents/pharmacology ; COVID-19 ; Humans ; Molecular Docking Simulation ; Pharmaceutical Preparations ; Phytochemicals/pharmacology ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Pharmaceutical Preparations ; Phytochemicals
Keywords	covid19
Language	English
Publishing date	2020-06-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1777901
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Article ; Online: Toward structure-multiple activity relationships (SMARts) using computational approaches: A polypharmacological perspective.

López-López, Edgar / Medina-Franco, José L

Drug discovery today

2024 , Page(s) 104046

Abstract: ... that computer-guided SMARts could contribute to the full automatization of drug design and drug repurposing ... repurposing of molecules. Computational methods have generated opportunities and challenges in medicinal ... space, in silico polypharmacology drug design approaches help to decode structure-multiple activity ...

Abstract	In the current era of biological big data, which are rapidly populating the biological chemical space, in silico polypharmacology drug design approaches help to decode structure-multiple activity relationships (SMARts). Current computational methods can predict or categorize multiple properties simultaneously, which aids the generation, identification, curation, prioritization, optimization, and repurposing of molecules. Computational methods have generated opportunities and challenges in medicinal chemistry, pharmacology, food chemistry, toxicology, bioinformatics, and chemoinformatics. It is anticipated that computer-guided SMARts could contribute to the full automatization of drug design and drug repurposing campaigns, facilitating the prediction of new biological targets, side and off-target effects, and drug-drug interactions.
Language	English
Publishing date	2024-05-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1324988-5
ISSN	1878-5832 ; 1359-6446
ISSN (online)	1878-5832
ISSN	1359-6446
DOI	10.1016/j.drudis.2024.104046
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Article ; Online: Computational and network pharmacology studies of

Chikhale, Rupesh V / Sinha, Saurabh K / Khanal, Pukar / Gurav, Nilambari S / Ayyanar, Muniappan / Prasad, Satyendra K / Wanjari, Manish M / Patil, Rajesh B / Gurav, Shailendra S

Phytomedicine plus : international journal of phytotherapy and phytopharmacology

2021 Volume 1, Issue 3, Page(s) 100095

Abstract: ... the significant role of repurposing existing drugs and natural lead in the treatment of COVID-19. The plant ... CoV-2. The network pharmacology analysis study confirmed these compounds' role in modulating ... accounted for about two million deaths. Several types of research are undergoing and have reported ...

Abstract	Background: Since December 2019, SARS-CoV-2 had been a significant threat globally, which has accounted for about two million deaths. Several types of research are undergoing and have reported the significant role of repurposing existing drugs and natural lead in the treatment of COVID-19. The plant Purpose: The present study was undertaken to investigate the potency of the several components of Methods: The docking simulation studies were carried out using Schrödinger maestro 2018-1 MM share version, while dynamics studies were conducted to understand the binding mechanism and the complexes' stability studies. Results: Out of sixty-six tested compounds, Chlorogenic acid, Quercitrin, and Myricetin were most effective in showing the highest binding energy against selected protein targets of SARS-CoV-2. The network pharmacology analysis study confirmed these compounds' role in modulating the immune response, inflammatory cascade, and cytokine storm through different signaling pathways. Conclusion: Current pharmacoinformatic approach shows possible role of
Language	English
Publishing date	2021-07-13
Publishing country	Netherlands
Document type	Journal Article
ISSN	2667-0313
ISSN (online)	2667-0313
DOI	10.1016/j.phyplu.2021.100095
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Article ; Online: Looking for SARS-CoV-2 Therapeutics Through Computational Approaches.

Vincenzi, Marian / Mercurio, Flavia Anna / Leone, Marilisa

Current medicinal chemistry

2022 Volume 30, Issue 28, Page(s) 3158–3214

Abstract: ... Objective: The present review aims to provide readers with a portrayal of computational approaches ... Background: In the last few years, in silico tools, including drug repurposing coupled ... has been devoted thus far to computationally targeting viral entry and searching for inhibitors ...

Abstract	Background: In the last few years, in silico tools, including drug repurposing coupled with structure-based virtual screening, have been extensively employed to look for anti-COVID-19 agents. Objective: The present review aims to provide readers with a portrayal of computational approaches that could be conducted more quickly and cheaply to novel anti-viral agents. Particular attention is given to docking-based virtual screening. Methods: The World Health Organization website was consulted to gain the latest information on SARS-CoV-2, its novel variants and their interplay with COVID-19 severity and treatment options. The Protein Data Bank was explored to look for 3D coordinates of SARS-CoV-2 proteins in their free and bound states, in the wild-types and mutated forms. Recent literature related to in silico studies focused on SARS-CoV-2 proteins was searched through PubMed. Results: A large amount of work has been devoted thus far to computationally targeting viral entry and searching for inhibitors of the S-protein/ACE2 receptor complex. Another large area of investigation is linked to in silico identification of molecules able to block viral proteases -including Mpro- thus avoiding maturation of proteins crucial for virus life cycle. Such computational studies have explored the inhibitory potential of the most diverse molecule databases (including plant extracts, dietary compounds, FDA approved drugs). Conclusion: More efforts need to be dedicated in the close future to experimentally validate the therapeutic power of in silico identified compounds in order to catch, among the wide ensemble of computational hits, novel therapeutics to prevent and/or treat COVID- 19.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Molecular Docking Simulation ; Protease Inhibitors/pharmacology ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Drug Repositioning
Chemical Substances	Protease Inhibitors ; Antiviral Agents
Language	English
Publishing date	2022-10-05
Publishing country	United Arab Emirates
Document type	Review ; Journal Article
ZDB-ID	1319315-6
ISSN	1875-533X ; 0929-8673
ISSN (online)	1875-533X
ISSN	0929-8673
DOI	10.2174/0929867329666221004104430
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Article ; Online: A systematic review of computational approaches to understand cancer biology for informed drug repurposing.

Ahmed, Faheem / Samantasinghar, Anupama / Soomro, Afaque Manzoor / Kim, Sejong / Choi, Kyung Hyun

Journal of biomedical informatics

2023 Volume 142, Page(s) 104373

Abstract: ... we present case studies of drug repurposing, discussing their limitations and offering recommendations ... developing effective treatments. One such approach is drug repurposing, which offers a shorter drug ... etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and ...

Abstract	Cancer is the second leading cause of death globally, trailing only heart disease. In the United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, the success rate for new cancer drug development remains less than 10%, making the disease particularly challenging. This low success rate is largely attributed to the complex and poorly understood nature of cancer etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and developing effective treatments. One such approach is drug repurposing, which offers a shorter drug development timeline and lower costs while increasing the likelihood of success. In this review, we provide a comprehensive analysis of computational approaches for understanding cancer biology, including systems biology, multi-omics, and pathway analysis. Additionally, we examine the use of these methods for drug repurposing in cancer, including the databases and tools that are used for cancer research. Finally, we present case studies of drug repurposing, discussing their limitations and offering recommendations for future research in this area.
MeSH term(s)	Humans ; Drug Repositioning/methods ; Systems Biology/methods ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Neoplasms/drug therapy ; Drug Development ; Computational Biology/methods
Chemical Substances	Antineoplastic Agents
Language	English
Publishing date	2023-04-27
Publishing country	United States
Document type	Systematic Review ; Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2057141-0
ISSN	1532-0480 ; 1532-0464
ISSN (online)	1532-0480
ISSN	1532-0464
DOI	10.1016/j.jbi.2023.104373
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Article ; Online: Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors.

Rampogu, Shailima / Jung, Tae Sung / Ha, Min Woo / Lee, Keun Woo

Scientific reports

2023 Volume 13, Issue 1, Page(s) 10583

Abstract: ... To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose ... polymerase inhibitors were used for this purpose and were repurposed against the main protease (Mpro) target ... and olaparib 1885, and rucaparib 184 demonstrated better CDOCKER docking scores for Mpro ...

Abstract	Coronavirus disease 2019 (COVID-19) is a recent pandemic that caused serious global emergency. To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose) polymerase inhibitors were used for this purpose and were repurposed against the main protease (Mpro) target of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). The results from these studies were used to design compounds using the 'Grow Scaffold' modules available on Discovery Studio v2018. The three designed compounds, olaparib 1826 and olaparib 1885, and rucaparib 184 demonstrated better CDOCKER docking scores for Mpro than their parent compounds. Moreover, the compounds adhered to Lipinski's rule of five and demonstrated a synthetic accessibility score of 3.55, 3.63, and 4.30 for olaparib 1826, olaparib 1885, and rucaparib 184, respectively. The short-range Coulombic and Lennard-Jones potentials also support the potential binding of the modified compounds to Mpro. Therefore, we propose these three compounds as novel SARS-CoV-2 inhibitors.
MeSH term(s)	Humans ; SARS-CoV-2 ; Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; COVID-19 ; Drug Repositioning ; Pandemics
Chemical Substances	Poly(ADP-ribose) Polymerase Inhibitors
Language	English
Publishing date	2023-06-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-36342-7
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Article ; Online: Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology.

Grasso, Daniela / Galderisi, Silvia / Santucci, Annalisa / Bernini, Andrea

International journal of molecular sciences

2023 Volume 24, Issue 6

Abstract: ... approaches regarding protein stability evaluation, binding pocket discovery and druggability, drug ... repurposing, and virtual ligand screening. The tools are presented as organized in an ideal workflow oriented ... and its misfolding and refolding. Such research can take advantage of computational methods ...

Abstract	Whenever a protein fails to fold into its native structure, a profound detrimental effect is likely to occur, and a disease is often developed. Protein conformational disorders arise when proteins adopt abnormal conformations due to a pathological gene variant that turns into gain/loss of function or improper localization/degradation. Pharmacological chaperones are small molecules restoring the correct folding of a protein suitable for treating conformational diseases. Small molecules like these bind poorly folded proteins similarly to physiological chaperones, bridging non-covalent interactions (hydrogen bonds, electrostatic interactions, and van der Waals contacts) loosened or lost due to mutations. Pharmacological chaperone development involves, among other things, structural biology investigation of the target protein and its misfolding and refolding. Such research can take advantage of computational methods at many stages. Here, we present an up-to-date review of the computational structural biology tools and approaches regarding protein stability evaluation, binding pocket discovery and druggability, drug repurposing, and virtual ligand screening. The tools are presented as organized in an ideal workflow oriented at pharmacological chaperones' rational design, also with the treatment of rare diseases in mind.
MeSH term(s)	Protein Folding ; Molecular Chaperones/metabolism ; Protein Conformation ; Biology ; Computational Biology
Chemical Substances	Molecular Chaperones
Language	English
Publishing date	2023-03-18
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24065819
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Article ; Online: Computational repurposing of oncology drugs through off-target drug binding interactions from pharmacological databases.

Walpole, Imogen R / Zaman, Farzana Y / Zhao, Peinan / Marshall, Vikki M / Lin, Frank P / Thomas, David M / Shackleton, Mark / Antolin, Albert A / Ameratunga, Malaka

Clinical and translational medicine

2024 Volume 14, Issue 4, Page(s) e1657

Abstract: ... with a known Food and Drug Administration (FDA)-approved biomarker. The computational repurposing approach was ... databases Probe Miner (PM), Broad Institute Drug Repurposing Hub (Broad Institute DRH) and TOPOGRAPH. GOF ... drug repurposing approach may assist in identifying novel repurposing events in cancer patients with no ...

Abstract	Purpose: Systematic repurposing of approved medicines for another indication may accelerate drug development in oncology. We present a strategy combining biomarker testing with drug repurposing to identify new treatments for patients with advanced cancer. Methods: Tumours were sequenced with the Illumina TruSight Oncology 500 (TSO-500) platform or the FoundationOne CDx panel. Mutations were screened by two medical oncologists and pathogenic mutations were categorised referencing literature. Variants of unknown significance were classified as potentially pathogenic using plausible mechanisms and computational prediction of pathogenicity. Gain of function (GOF) mutations were evaluated through repurposing databases Probe Miner (PM), Broad Institute Drug Repurposing Hub (Broad Institute DRH) and TOPOGRAPH. GOF mutations were repurposing events if identified in PM, not indexed in TOPOGRAPH and excluding mutations with a known Food and Drug Administration (FDA)-approved biomarker. The computational repurposing approach was validated by evaluating its ability to identify FDA-approved biomarkers. The total repurposable genome was identified by evaluating all possible gene-FDA drug-approved combinations in the PM dataset. Results: The computational repurposing approach was accurate at identifying FDA therapies with known biomarkers (94%). Using next-generation sequencing molecular reports (n = 94), a meaningful percentage of patients (14%) could have an off-label therapeutic identified. The frequency of theoretical drug repurposing events in The Cancer Genome Atlas pan-cancer dataset was 73% of the samples in the cohort. Conclusion: A computational drug repurposing approach may assist in identifying novel repurposing events in cancer patients with no access to standard therapies. Further validation is needed to confirm a precision oncology approach using drug repurposing.
MeSH term(s)	Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Drug Repositioning ; Precision Medicine ; Pharmaceutical Preparations ; Biomarkers
Chemical Substances	Pharmaceutical Preparations ; Biomarkers
Language	English
Publishing date	2024-04-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2697013-2
ISSN	2001-1326 ; 2001-1326
ISSN (online)	2001-1326
ISSN	2001-1326
DOI	10.1002/ctm2.1657
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Article ; Online: An Overview of SARS-CoV-2 Potential Targets, Inhibitors, and Computational Insights to Enrich the Promising Treatment Strategies.

Kumawat, Pooja / Agarwal, Lokesh Kumar / Sharma, Kuldeep

Current microbiology

2024 Volume 81, Issue 7, Page(s) 169

Abstract: ... Overall, the present in-depth review aims to expedite the process of identifying and repurposing drugs ... to combat COVID-19. Investigating the potential targets, inhibitors, and in silico approaches pertinent ... approved drugs. This article reviews the viral enzymes and their counter receptors involved in the entry of SARS ...

Abstract	The rapid spread of the SARS-CoV-2 virus has emphasized the urgent need for effective therapies to combat COVID-19. Investigating the potential targets, inhibitors, and in silico approaches pertinent to COVID-19 are of utmost need to develop novel therapeutic agents and reprofiling of existing FDA-approved drugs. This article reviews the viral enzymes and their counter receptors involved in the entry of SARS-CoV-2 into host cells, replication of genomic RNA, and controlling the host cell physiology. In addition, the study provides an overview of the computational techniques such as docking simulations, molecular dynamics, QSAR modeling, and homology modeling that have been used to find the FDA-approved drugs and other inhibitors against SARS-CoV-2. Furthermore, a comprehensive overview of virus-based and host-based druggable targets from a structural point of view, together with the reported therapeutic compounds against SARS-CoV-2 have also been presented. The current study offers future perspectives for research in the field of network pharmacology investigating the large unexplored molecular libraries. Overall, the present in-depth review aims to expedite the process of identifying and repurposing drugs for researchers involved in the field of COVID-19 drug discovery.
MeSH term(s)	SARS-CoV-2/drug effects ; Antiviral Agents/pharmacology ; Antiviral Agents/chemistry ; Humans ; COVID-19 Drug Treatment ; Molecular Docking Simulation ; COVID-19/virology ; Drug Repositioning ; Virus Internalization/drug effects ; Molecular Dynamics Simulation
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2024-05-11
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-024-03671-3
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Article ; Online: Drug repurposing against SARS-CoV-2 using computational approaches.

Kumar, Sumit / Kovalenko, Svitlana / Bhardwaj, Shakshi / Sethi, Aaftaab / Gorobets, Nikolay Yu / Desenko, Sergey M / Poonam / Rathi, Brijesh

Drug discovery today

2022 Volume 27, Issue 7, Page(s) 2015–2027

Abstract: ... of these targets and their available potential inhibitors predicted by the computational approaches. Among the hits ... identified by computational approaches, 35 candidates were suggested for further evaluation, among which ten ... drugs are in clinical trials (Phase III and IV) for treating Coronavirus 2019 (COVID-19). ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has generated a critical need for treatments to reduce morbidity and mortality associated with this disease. However, traditional drug development takes many years, which is not practical solution given the current pandemic. Therefore, a viable option is to repurpose existing drugs. The structural data of several proteins vital for the virus became available shortly after the start of the pandemic. In this review, we discuss the importance of these targets and their available potential inhibitors predicted by the computational approaches. Among the hits identified by computational approaches, 35 candidates were suggested for further evaluation, among which ten drugs are in clinical trials (Phase III and IV) for treating Coronavirus 2019 (COVID-19).
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; SARS-CoV-2 ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2022-02-10
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1324988-5
ISSN	1878-5832 ; 1359-6446
ISSN (online)	1878-5832
ISSN	1359-6446
DOI	10.1016/j.drudis.2022.02.004
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