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Verma K, Lahariya AK, Verma G, Kumari M, Gupta D, Maurya N, Verma AK, Mani A, Schneider KA, Bharti PK. Screening of potential antiplasmodial agents targeting cysteine protease-Falcipain 2: a computational pipeline. J Biomol Struct Dyn 2023; 41:8121-8164. [PMID: 36218071 DOI: 10.1080/07391102.2022.2130984] [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: 07/13/2022] [Accepted: 09/24/2022] [Indexed: 10/17/2022]
Abstract
The spread of antimalarial drug resistance is a substantial challenge in achieving global malaria elimination. Consequently, the identification of novel therapeutic candidates is a global health priority. Malaria parasite necessitates hemoglobin degradation for its survival, which is mediated by Falcipain 2 (FP2), a promising antimalarial target. In particular, FP2 is a key enzyme in the erythrocytic stage of the parasite's life cycle. Here, we report the screening of approved drugs listed in DrugBank using a computational pipeline that includes drug-likeness, toxicity assessments, oral toxicity evaluation, oral bioavailability, docking analysis, maximum common substructure (MCS) and molecular dynamics (MD) Simulations analysis to identify capable FP2 inhibitors, which are hence potential antiplasmodial agents. A total of 45 drugs were identified, which have positive drug-likeness, no toxic features and good bioavailability. Among these, six drugs showed good binding affinity towards FP2 compared to E64, an epoxide known to inhibit FP2. Notably, two of them, Cefalotin and Cefoxitin, shared the highest MCS with E64, which suggests that they possess similar biological activity as E64. In an investigation using MD for 100 ns, Cefalotin and Cefoxitin showed adequate protein compactness as well as satisfactory complex stability. Overall, these computational approach findings can be applied for designing and developing specific inhibitors or new antimalarial agents for the treatment of malaria infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanika Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Ayush Kumar Lahariya
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Garima Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- School of Studies in Microbiology, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Monika Kumari
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Biotechnology, St. Aloysius' (Autonomous) College, Affiliated to Rani Durgawati University, Jabalpur, Madhya Pradesh, Jabalpur, India
| | - Divanshi Gupta
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Biological Sciences, Rani Durgawati University, Jabalpur, Madhya Pradesh, India
| | - Neha Maurya
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, India
| | - Anil Kumar Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, India
| | | | - Praveen Kumar Bharti
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Parasite Host Biology, National Institute of Malaria Research, Delhi, India
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Drug Repositioning and Subgroup Discovery for Precision Medicine Implementation in Triple Negative Breast Cancer. Cancers (Basel) 2021; 13:cancers13246278. [PMID: 34944904 PMCID: PMC8699385 DOI: 10.3390/cancers13246278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/29/2022] Open
Abstract
Simple Summary The heterogeneity of complicated diseases like cancer negatively affects patients’ responses to treatment. Finding homogeneous subgroups of patients within the cancer population and finding the appropriate treatment for each subgroup will improve patients’ survival. In this study, we focus on triple-negative breast cancer (TNBC), where approximately 80% of patients do not entirely respond to chemotherapy. Our aim is to find subgroups of TNBC patients and identify drugs that have the potential to tailor treatments for each group through drug repositioning. After applying our method to TNBC, we found that different targeted mechanisms were suggested for different groups of patients. Our findings could help the research community to gain a better understanding of different subgroups within the TNBC population and can help the drugs to be repurposed with explainable results regarding the targeted mechanism. Abstract Breast cancer (BC) is the leading cause of death among female patients with cancer. Patients with triple-negative breast cancer (TNBC) have the lowest survival rate. TNBC has substantial heterogeneity within the BC population. This study utilized our novel patient stratification and drug repositioning method to find subgroups of BC patients that share common genetic profiles and that may respond similarly to the recommended drugs. After further examination of the discovered patient subgroups, we identified five homogeneous druggable TNBC subgroups. A drug repositioning algorithm was then applied to find the drugs with a high potential for each subgroup. Most of the top drugs for these subgroups were chemotherapy used for various types of cancer, including BC. After analyzing the biological mechanisms targeted by these drugs, ferroptosis was the common cell death mechanism induced by the top drugs in the subgroups with neoplasm subdivision and race as clinical variables. In contrast, the antioxidative effect on cancer cells was the common targeted mechanism in the subgroup of patients with an age less than 50. Literature reviews were used to validate our findings, which could provide invaluable insights to streamline the drug repositioning process and could be further studied in a wet lab setting and in clinical trials.
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Verma K, Lahariya AK, Dubey S, Verma AK, Das A, Schneider KA, Bharti PK. An integrated virtual screening and drug repurposing strategy for the discovery of new antimalarial drugs against Plasmodium falciparum phosphatidylinositol 3-kinase. J Cell Biochem 2021; 122:1326-1336. [PMID: 33998049 DOI: 10.1002/jcb.29954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 11/10/2022]
Abstract
The emergence and spread of drug resistance in Plasmodium falciparum, the parasite causing the most severe form of human malaria, is a major threat to malaria control and elimination programs around the globe. With P. falciparum having evolved widespread resistance against a number of previously widely used drugs, currently, artemisinin (ART) and its derivatives are the cornerstones of first-line treatments of uncomplicated malaria. However, growing incidences of ART failure reflect the spread of ART-resistant P. falciparum strains. Despite current efforts to understand the primary cause of ART resistance due to mutations in the Kelch 13 gene (PfK13), the mechanism underlying ART resistance is still not completely unclear and no feasible strategies to counteract the causes and thereby restoring the efficiency of ART have been developed. We use a polypharmacology approach to identify potential drugs that can be used for the novel purpose (target). Of note, we have designed a multimodal stratagem to identify approved drugs with a potential antimalarial activity using computational drug reprofiling. Our investigations suggest that oxetacaine, simvastatin, repaglinide, aclidinium, propafenone, and lovastatin could be repurposed for malaria control and prevention.
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Affiliation(s)
- Kanika Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Ayush K Lahariya
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Shivangee Dubey
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Anil K Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Aparup Das
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | | | - Praveen K Bharti
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
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Avti P, Chauhan A, Shekhar N, Prajapat M, Sarma P, Kaur H, Bhattacharyya A, Kumar S, Prakash A, Sharma S, Medhi B. Computational basis of SARS-CoV 2 main protease inhibition: an insight from molecular dynamics simulation based findings. J Biomol Struct Dyn 2021; 40:8894-8904. [PMID: 33998950 PMCID: PMC8127165 DOI: 10.1080/07391102.2021.1922310] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by newly discovered severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). One of the striking targets amongst all the proteins in coronavirus is the main protease (Mpro), as it plays vital biological roles in replication and maturation of the virus, and hence the potential target. The aim of this study is to repurpose the Food and Drug Administration (FDA) approved molecules via computer-aided drug designing against Mpro (PDB ID: 6Y2F) of SARS CoV-2 due to its high x-ray resolution of 1.95 Å as compared to other published Mprostructures. High Through Virtual Screening (HTVS) of 2456 FDA approved drugs using structure-based docking were analyzed. Molecular Dynamics simulations were performed to check the overall structural stability (RMSD), Cα fluctuations (RMSF) and protein-ligand interactions. Further, trajectory analysis was performed to assess the binding quality by exploiting the protein-residue motion cross correlation (DCCM) and binding free energy (MM/GBSA). Tenofovir, an antiretroviral for HIV-proteases and Terlipressin, a vasoconstrictor show stable RMSD, RMSF, better MM/GBSA with good cross correlation as compared to the Apo and O6K. Moreover, the results show concurrence with Nelfinavir, Lopinavir and Ritonavir which have shown significant inhibition in in vitro studies. Therefore, we conclude that Tenofovir and Terlipresssin might also show protease inhibition but are still open to clinical validation in case of SARS-CoV 2 treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saurabh Sharma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India,CONTACT Bikash Medhi Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Correia AS, Gärtner F, Vale N. Drug combination and repurposing for cancer therapy: the example of breast cancer. Heliyon 2021; 7:e05948. [PMID: 33490692 PMCID: PMC7810770 DOI: 10.1016/j.heliyon.2021.e05948] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 12/30/2022] Open
Abstract
Cancer is a set of extremely complex diseases, which are increasingly prominent today, as it affects and kills millions of people worldwide, being the subject of intense study both in its pathophysiology and therapy. Especially in women, breast cancer is still a cancer with a high incidence and mortality. Even though mortality rates for this type of cancer have declined in recent years, it remains challenging at the treatment level, especially the metastatic type. Due to all the impact on health, cancer therapy is the subject of costly and intense research. To enrich this therapy, as well as decrease its underlying high associated costs, drug repurposing and drug combinations are strategies that have been increasingly studied and addressed. As the name implies, drug repurposing presupposes giving new purposes to agents which, in this case, are approved for the therapy of other diseases (for example, cardiovascular or metabolic diseases), but are not approved for cancer therapy. Therefore, a better knowledge of these therapeutic modalities for breast cancer therapy is crucial for improved therapy. In this particular review, we will discuss some relevant aspects of cancer and, particularly, breast cancer and its therapy. Also, drug combination and repurposing will be highlighted, together with relevant examples. Despite some limitations that need to be overcome, these methodologies are extremely important and advantageous in combating several current problems of cancer therapy, namely in terms of costs and resistance to current therapeutic modalities. These approaches will be explored with a special focus on breast cancer.
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Affiliation(s)
- Ana Salomé Correia
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Dr. Plácido da Costa, 4200-450 Porto, Portugal
- Department of Molecular Pathology and Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Fátima Gärtner
- Department of Molecular Pathology and Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
| | - Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Dr. Plácido da Costa, 4200-450 Porto, Portugal
- Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
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Abstract
Drug repurposing is a powerful technique which has been recently employed in both industry and academia to discover and validate previously approved drugs for new indications. It provides the quickest possible transition from bench to bedside. In essence, computational strategies are appealing because they putatively nominate the most encouraging candidate for a given indication. A wide range of computational methods exist for repositioning. In this chapter we present the guidelines for performing integrated drug repurposing strategy by combining disease-disease association and molecular simulation analysis.
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