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Sarkar M, Raj R R, Maliekal TT. Finding the partner: FRET and beyond. Exp Cell Res 2024; 441:114166. [PMID: 39029572 DOI: 10.1016/j.yexcr.2024.114166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
Given the importance of aberrant protein-protein interactions (PPIs) in disease, the recent drug discovery focuses on targeting the altered PPIs to treat the disease. In this context, identifying the atypical PPIs underlying the disease is critical for the development of diagnostics and therapeutics. Various biochemical, biophysical, and genetic methods have been reported to study PPIs. Here, we are giving a short account of those techniques with more emphasis on Förster resonance energy transfer (FRET), which can be used to monitor macromolecular interactions in live cells. Besides the basics of FRET, we explain the modifications of its application, like Single molecule FRET (smFRET), Fluorescence Lifetime Imaging Microscopy-FRET (FLIM-FRET), and photoswitching FRET. While smFRET is extensively used for evaluating the biology of nucleic acids and also to develop diagnostics, FLIM-FRET is widely exploited to study the PPIs underlying neurological disorders and cancer. Photoswitching FRET is a relatively newer technique and it has tremendous potential to unravel the significance of different PPIs. Besides these modifications, there are several advancements in the field by introducing new fluorophores. Identification of lanthanide chelates, quantum dots, and other nanoparticle fluorophores has revolutionized the applications of FRET in diagnostics and basic biology. Yet, these methods can be employed to study the interactions of only two molecules. Since the majority of the PPIs are multimeric complexes, we still need to improve our technologies to study these interactions in live cells in real-time.
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Affiliation(s)
- Meghna Sarkar
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Reshma Raj R
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India.
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2
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Ikram S, Sayyah E, Durdağı S. Identifying Potential SOS1 Inhibitors via Virtual Screening of Multiple Small Molecule Libraries against KRAS-SOS1 Interaction. Chembiochem 2024; 25:e202400008. [PMID: 38622060 DOI: 10.1002/cbic.202400008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
The RAS-MAPK signaling pathway, crucial for cell proliferation and differentiation, involves key proteins KRAS and SOS1. Mutations in the KRAS and SOS1 genes are implicated in various cancer types, including pancreatic, lung, and juvenile myelomonocytic leukemia. There is considerable interest in identifying inhibitors targeting KRAS and SOS1 to explore potential therapeutic strategies for cancer treatment. In this study, advanced in silico techniques were employed to screen small molecule libraries at this interface, leading to the identification of promising lead compounds as potential SOS1 inhibitors. Comparative analysis of the average binding free energies of these predicted potent compounds with known SOS1 small molecule inhibitors revealed that the identified compounds display similar or even superior predicted binding affinities compared to the known inhibitors. These findings offer valuable insights into the potential of these compounds as candidates for further development as effective anti-cancer agents.
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Affiliation(s)
- Saima Ikram
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
| | - Ehsan Sayyah
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
| | - Serdar Durdağı
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34734, Istanbul, Turkey
- Lab for Innovative Drugs (Lab4IND), Computational Drug Design Center (HİTMER), Bahçeşehir University, 34734, İstanbul, Türkiye
- Molecular Therapy Lab (MTL), Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, 34353, Istanbul, Türkiye
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3
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Marques RE, Shimizu JF, Nogueira ML, Vasilakis N. Current challenges in the discovery of treatments against Mayaro fever. Expert Opin Ther Targets 2024; 28:345-356. [PMID: 38714500 PMCID: PMC11189740 DOI: 10.1080/14728222.2024.2351504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/01/2024] [Indexed: 05/10/2024]
Abstract
INTRODUCTION Mayaro fever is an emerging viral disease that manifests as an acute febrile illness. The disease is self-limiting, however joint pain can persist for months leading to chronic arthralgia. There is no specific treatment available, which ultimately leads to socioeconomic losses in populations at risk as well as strains to the public health systems. AREAS COVERED We reviewed the candidate treatments proposed for Mayaro virus (MAYV) infection and disease, including antiviral compounds targeting viral or host mechanisms, and pathways involved in disease development and pathogenicity. We assessed compound screening technologies and experimental infection models used in these studies and indicated the advantages and limitations of available technologies and intended therapeutic strategies. EXPERT OPINION Although several compounds have been suggested as candidate treatments against MAYV infection, notably those with antiviral activity, most compounds were assessed only in vitro. Compounds rarely progress toin vivo or preclinical studies, and such difficulty may be associated with limited experimental models. MAYV biology is largely inferred from related alphaviruses and reflected by few studies focusing on target proteins or mechanisms of action for MAYV. Therapeutic strategies targeting pathogenic inflammatory responses have shown potential against MAYV-induced disease in vivo, which might reduce long-term sequelae.
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Affiliation(s)
- Rafael Elias Marques
- Brazilian Biosciences National Laboratory – LNBio, Brazilian Center for Research in Energy and Materials – CNPEM, Campinas, São Paulo, Brazil
| | - Jacqueline Farinha Shimizu
- Brazilian Biosciences National Laboratory – LNBio, Brazilian Center for Research in Energy and Materials – CNPEM, Campinas, São Paulo, Brazil
| | - Maurício Lacerda Nogueira
- Faculdade de Medicina de São Jose do Rio Preto - FAMERP, São Jose do Rio Preto, São Paulo, Brazil
- University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Nikos Vasilakis
- University of Texas Medical Branch at Galveston, Galveston, Texas, USA
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Dakkak BE, Taneera J, El-Huneidi W, Abu-Gharbieh E, Hamoudi R, Semreen MH, Soares NC, Abu-Rish EY, Alkawareek MY, Alkilany AM, Bustanji Y. Unlocking the Therapeutic Potential of BCL-2 Associated Protein Family: Exploring BCL-2 Inhibitors in Cancer Therapy. Biomol Ther (Seoul) 2024; 32:267-280. [PMID: 38589288 PMCID: PMC11063480 DOI: 10.4062/biomolther.2023.149] [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: 08/25/2023] [Revised: 11/05/2023] [Accepted: 12/05/2023] [Indexed: 04/10/2024] Open
Abstract
Apoptosis, programmed cell death pathway, is a vital physiological mechanism that ensures cellular homeostasis and overall cellular well-being. In the context of cancer, where evasion of apoptosis is a hallmark, the overexpression of anti-apoptotic proteins like Bcl2, Bcl-xL and Mcl-1 has been documented. Consequently, these proteins have emerged as promising targets for therapeutic interventions. The BCL-2 protein family is central to apoptosis and plays a significant importance in determining cellular fate serving as a critical determinant in this biological process. This review offers a comprehensive exploration of the BCL-2 protein family, emphasizing its dual nature. Specifically, certain members of this family promote cell survival (known as anti-apoptotic proteins), while others are involved in facilitating cell death (referred to as pro-apoptotic and BH3-only proteins). The potential of directly targeting these proteins is examined, particularly due to their involvement in conferring resistance to traditional cancer therapies. The effectiveness of such targeting strategies is also discussed, considering the tumor's propensity for anti-apoptotic pathways. Furthermore, the review highlights emerging research on combination therapies, where BCL-2 inhibitors are used synergistically with other treatments to enhance therapeutic outcomes. By understanding and manipulating the BCL-2 family and its associated pathways, we open doors to innovative and more effective cancer treatments, offering hope for resistant and aggressive cases.
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Affiliation(s)
- Bisan El Dakkak
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon 1649-016, Portugal
| | - Eman Y. Abu-Rish
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | | | | | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
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Doğan N, Yavuz SÇ, Sahin K, Orhan MD, Muhammed HK, Calis S, Küp FÖ, Avsar T, Akkoc S, Tapera M, Sahin O, Kilic T, Durdagi S, Saripinar E. Synthesis, Characterization, Biological Activity and Molecular Modeling Studies of Novel Aminoguanidine Derivatives. ChemistrySelect 2022. [DOI: 10.1002/slct.202202819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Nuriye Doğan
- Department of Chemistry Erciyes University Kayseri Türkiye
| | - Sevtap Çağlar Yavuz
- Department of Medical Services and Technicians İliç Dursun Yıldırım Vocational School Erzincan Binali Yıldırım University 24700 Erzincan Türkiye
| | - Kader Sahin
- Computational Biology and Molecular Simulations Laboratory Department of Biophysics School of Medicine Bahcesehir University Istanbul Türkiye
- Department of Analytical Chemistry School of Pharmacy Bahcesehir University Istanbul Türkiye
| | - Muge Didem Orhan
- Department of Medical Biology School of Medicine Bahcesehir University Istanbul Türkiye
| | | | - Seyma Calis
- Department of Medical Biology School of Medicine Bahcesehir University Istanbul Türkiye
| | - Fatma Öztürk Küp
- Department of Biology Faculty of Science Erciyes University Kayseri Türkiye
| | - Timucin Avsar
- Department of Medical Biology School of Medicine Bahcesehir University Istanbul Türkiye
| | - Senem Akkoc
- Department of Basic Pharmaceutical Sciences Faculty of Pharmacy Suleyman Demirel University Isparta Türkiye
| | - Michael Tapera
- Department of Chemistry Erciyes University Kayseri Türkiye
| | - Onur Sahin
- Scientific and Technological Research Application and Research Center Sinop University Sinop Türkiye
| | - Turker Kilic
- Deperment of Neurosurgery School of Medicine Bahcesehir University Istanbul Türkiye
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory Department of Biophysics School of Medicine Bahcesehir University Istanbul Türkiye
- Department of Pharmaceutical Chemistry School of Pharmacy Bahcesehir University Istanbul Türkiye
| | - Emin Saripinar
- Department of Chemistry Erciyes University Kayseri Türkiye
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Ghosh A, Sarmah P, Patel H, Mukerjee N, Mishra R, Alkahtani S, Varma RS, Baishya D. Nonlinear molecular dynamics of quercetin in Gynocardia odorata and Diospyros malabarica fruits: Its mechanistic role in hepatoprotection. PLoS One 2022; 17:e0263917. [PMID: 35313329 PMCID: PMC8936497 DOI: 10.1371/journal.pone.0263917] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/31/2022] [Indexed: 12/28/2022] Open
Abstract
Liver performs number of critical physiological functions in human system. Intoxication of liver leads to accumulation of free radicals that eventually cause damage, fibrosis, cirrhosis and cancer. Carbon tetrachloride (CCl4) belongs to hepatotoxin is converted to a highly reactive free radical by cytochrome P450 enzymes that causes liver damage. Plant extracts derived quercetin has substantial role in hepatoprotection. This study highlights the possible mechanism by which quercetin plays significant role in hepatoprotection. HPLC analysis revealed the abundance of quercetin in the fruit extracts of Gynocardia odorata and Diospyros malabarica, were isolated, purified and subjected to liver function analysis on Wistar rats. Post quercetin treatment improved liver function parameters in the hepatotoxic Wistar rats by augmenting bilirubin content, SGOT and SGPT activity. Gene expression profile of quercetin treated rats revealed down regulation of HGF, TIMP1 and MMP2 expressed during CCl4 induction. In silico molecular mechanism prediction suggested that quercetin has a high affinity for cell signaling pathway proteins BCL-2, JAK2 and Cytochrome P450 Cyp2E1, which all play a significant role in CCl4 induced hepatotoxicity. In silico molecular docking and molecular dynamics simulation have shown that quercetin has a plausible affinity for major signaling proteins in liver. MMGBSA studies have revealed high binding of quercetin (ΔG) -41.48±11.02, -43.53±6.55 and -39.89±5.78 kcal/mol, with BCL-2, JAK2 and Cyp2E1, respectively which led to better stability of the quercetin bound protein complexes. Therefore, quercetin can act as potent inhibitor against CCl4 induced hepatic injury by regulating BCL-2, JAK2 and Cyp2E1.
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Affiliation(s)
- Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Pranjal Sarmah
- Department of Bioengineering and Technology, GUIST, Gauhati University, Guwahati, Assam, India
| | - Harun Patel
- R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharastra, India
| | - Nobendu Mukerjee
- Department of Microbiology; Ramakrishna Mission Vivekananda Centenary College, Khardaha, West Bengal, Kolkata, India
| | - Rajbardhan Mishra
- Laboratory of Immunotherapy, Institute of Microbiology v.v.i., Czech Academy of Sciences, Videnska, Prague, Czech Republic
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail: (DB); (SA)
| | - Rajender S. Varma
- Regional Center of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacky University, Olomouc, Czech Republic
| | - Debabrat Baishya
- Department of Bioengineering and Technology, GUIST, Gauhati University, Guwahati, Assam, India
- * E-mail: (DB); (SA)
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