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Dhanalakshmi B, Anil Kumar BM, Srinivasa Murthy V, Srinivasa SM, Vivek HK, Sennappan M, Rangappa S. Design, synthesis and docking studies of novel 4-aminophenol-1,2,4-oxadiazole hybrids as apoptosis inducers against triple negative breast cancer cells targeting MAP kinase. J Biomol Struct Dyn 2024; 42:5841-5857. [PMID: 37529915 DOI: 10.1080/07391102.2023.2239912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023]
Abstract
In our study, a series of novel 4-aminophenol benzamide-1,2,4-oxadiazole hybrid analogues have been designed and synthesized by condensing 4-hydroxyphenyl arylamides (3a-c) and 5-chloromethyl-3-aryl-1,2,4-oxadiazoles (6a-d). The structure of the synthesised compounds was verified by various spectroscopic techniques (1H NMR, 13C NMR, IR and LC-MS). All the prepared compounds were subjected to in silico and in vitro antiproliferative study against TNBC cell lines MDA-MB-468 and MDA-MB-231. The investigations revealed that compound 7k significantly promoted apoptosis against MDA-MB-468 and MDA-MB-231 cells with IC50 values of 22.31 µM and 26.27 µM, respectively. Compound 7k interacted with crucial active sites of MAPK and exhibited the highest docking score of -7.06 kcal/mol. Docking was validated with molecular dynamic studies with simulation for 100 ns, depicting various stable interactions with MAPK. Consequently, 7k forms stable H-Bonds and π-π stacking with amino acid residues along with π-cation. Our investigations reveal that the in vitro antiproliferative study of 7k was in good correlation with the in silico studies. Hence, 7k serves as a potential novel lead for the inhibition of TNBCs by downregulating MAPK P38.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Boregowda Dhanalakshmi
- Department of Chemistry, School of Engineering, Dayananda Sagar University, Bengaluru, Karnataka, India
- Department of Chemistry, Rajeev Institute of Technology, Visvesvaraya Technological University, Hassan, Karnataka, India
| | - Belagal Motatis Anil Kumar
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
| | | | - Sudhanva Muddenahalli Srinivasa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
| | - Hamse Kameshwar Vivek
- Department of Biochemistry, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Department of Biochemistry, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
| | - Madhappan Sennappan
- Department of Chemistry, Dayananda Sagar College of Engineering, Bangalore, Karnataka, India
| | - Shobith Rangappa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, B.G Nagara, Karnataka, India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B.G Nagara, Karnataka, India
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Kurnia D, Lestari S, Mayanti T, Gartika M, Nurdin D. Anti-Infection of Oral Microorganisms from Herbal Medicine of Piper crocatum Ruiz & Pav. Drug Des Devel Ther 2024; 18:2531-2553. [PMID: 38952486 PMCID: PMC11215520 DOI: 10.2147/dddt.s453375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/20/2024] [Indexed: 07/03/2024] Open
Abstract
The WHO Global Status Report on Oral Health 2022 reveals that oral diseases caused by infection with oral pathogenic microorganisms affect nearly 3.5 billion people worldwide. Oral health problems are caused by the presence of S. mutans, S. sanguinis, E. faecalis and C. albicans in the oral cavity. Synthetic anti-infective drugs have been widely used to treat oral infections, but have been reported to cause side effects and resistance. Various strategies have been implemented to overcome this problem. Synthetic anti-infective drugs have been widely used to treat oral infections, but they have been reported to cause side effects and resistance. Therefore, it is important to look for safe anti-infective alternatives. Ethnobotanical and ethnopharmacological studies suggest that Red Betel leaf (Piper crocatum Ruiz & Pav) could be a potential source of oral anti-infectives. This review aims to discuss the pathogenesis mechanism of several microorganisms that play an important role in causing health problems, the mechanism of action of synthetic oral anti-infective drugs in inhibiting microbial growth in the oral cavity, and the potential of red betel leaf (Piper crocatum Ruiz & Pav) as an herbal oral anti-infective drug. This study emphasises the importance of researching natural components as an alternative treatment for oral infections that is more effective and can meet global needs.
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Affiliation(s)
- Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Seftiana Lestari
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Tri Mayanti
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Meirina Gartika
- Department of Pediatric Dentistry, Faculty of Medicine, University of Padjadjaran, Bandung, Indonesia
| | - Denny Nurdin
- Departement of Conservative Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
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Ghafoor D, Zeb A, Ali SS, Ali M, Akbar F, Ud Din Z, Ur Rehman S, Suleman M, Khan W. Immunoinformatic based designing of potential immunogenic novel mRNA and peptide-based prophylactic vaccines against H5N1 and H7N9 avian influenza viruses. J Biomol Struct Dyn 2024; 42:3641-3658. [PMID: 37222664 DOI: 10.1080/07391102.2023.2214228] [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: 10/31/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Influenza viruses are the most common cause of serious respiratory illnesses worldwide and are responsible for a significant number of annual fatalities. Therefore, it is crucial to look for new immunogenic sites that might trigger an effective immune response. In the present study, bioinformatics tools were used to design mRNA and multiepitope-based vaccines against H5N1 and H7N9 subtypes of avian influenza viruses. Several Immunoinformatic tools were employed to extrapolate T and B lymphocyte epitopes of HA and NA proteins of both subtypes. The molecular docking approach was used to dock the selected HTL and CTL epitopes with the corresponding MHC molecules. Eight (8) CTL, four (4) HTL, and Six (6) linear B cell epitopes were chosen for the structural arrangement of mRNA and of peptide-based prophylactic vaccine designs. Different physicochemical characteristics of the selected epitopes fitted with suitable linkers were analyzed. High antigenic, non-toxic, and non-allergenic features of the designed vaccines were noted at a neutral physiological pH. Codon optimization tool was used to check the GC content and CAI value of constructed MEVC-Flu vaccine, which were recorded to be 50.42% and 0.97 respectively. the GC content and CAI value verify the stable expression of vaccine in pET28a + vector. In-silico immunological simulation the MEVC-Flu vaccine construct revealed a high level of immune responses. The molecular dynamics simulation and docking results confirmed the stable interaction of TLR-8 and MEVC-Flu vaccine. Based on these parameters, vaccine constructs can be regarded as an optimistic choice against H5N1 and H7N9 strains of the influenza virus. Further experimental testing of these prophylactic vaccine designs against pathogenic avian influenza strains may clarify their safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dawood Ghafoor
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Wuhan, Hubei, China
| | - Adnan Zeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ud Din
- Center for Advanced Studies in Vaccinology and Biotechnology, University of Balochistan Quetta, Quetta, Pakistan
| | - Shoaib Ur Rehman
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Wajid Khan
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
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Vemula D, Mohanty S, Bhandari V. Repurposing of Food and Drug Admnistration (FDA) approved library to identify a potential inhibitor of trypanothione synthetase for developing an antileishmanial agent. Heliyon 2024; 10:e27602. [PMID: 38509977 PMCID: PMC10951594 DOI: 10.1016/j.heliyon.2024.e27602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Leishmaniasis is one of the top 10 neglected tropical diseases. Globally, it impacts more than 12 million individuals. In light of the absence of a safer, affordable treatment for the Leishmaniasis, along with therapeutic failures and drug resistance, novel therapeutic strategies are necessary to discover new drugs. Treatment would benefit by concentrating on the precise targets that are crucial for the parasite to survive. A target that aids in the organism's survival under oxidative stress is trypanothione synthetase (TyS), which is a component of the trypanothione pathway in Leishmania spp. To find potential TyS inhibitors for the purpose of discovering novel antileishmanial drugs, we used a virtual screening strategy. Using the Glide module of Schrodinger-suite 2023, an FDA-approved library containing 2000 drugs from the ZINC-15 database was screened against the TyS. Dostinex, raloxifene, and formoterol showed good docking scores of -10.568 kcal/mol, -10.446 kcal/mol, and -56.21 kcal/mol, as well as good binding energies of -70.41 kcal/mol, -56.21 kcal/mol, and -64.15 kcal/mol respectively. The stability of the ligand-protein complexes was assessed further with the help of Desmond to execute a 100-ns molecular dynamics simulation. The Prime module was utilised to perform post-MM/GBSA analysis on these three molecules along with the toxicity profiling using Protox II web server. This study suggests that dostinex, formoterol, and raloxifene may act as effective inhibitors of the TyS receptor which could be used as novel antileishmanial agents for the therapeutic applications. Thorough preclinical studies are necessary to confirm the identified compounds chemotherapeutic qualities.
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Affiliation(s)
| | | | - Vasundhra Bhandari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hyderabad, India
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Ngoc Mai TT, Minh PN, Phat NT, Duong TH, Minh An TN, Dang VS, Van Hue N, Tri MD. Antimicrobial and alpha-glucosidase inhibitory flavonoid glycosides from the plant Mussaenda recurvata: in vitro and in silico approaches. RSC Adv 2024; 14:9326-9338. [PMID: 38505391 PMCID: PMC10950057 DOI: 10.1039/d4ra00666f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/05/2024] [Indexed: 03/21/2024] Open
Abstract
Seven flavonoid glycosides were isolated from the aerial portions of Mussaenda recurvata during a phytochemical analysis. This comprised one novel component, ecurvoside, and six well-studied compounds, namely astragalin, isoquercitrin, nicotiflorin, rutin, hesperidin, and neohesperidin. The chemical structures of compounds were identified using spectroscopic techniques and a comparison with previously published studies. Alpha-glucosidase inhibition testing was carried out on all isolated compounds. The compounds evaluated have IC50 values between 35.6 and 239.1 g mL-1, indicating a moderate degree of inhibition. In vitro antimicrobial activities of compounds 1-7 have screened against the bacteria Pseudomonas aeruginosa (P. aeruginosa), methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus faecalis (Strep. faecalis), and fungi: Candida albicans (C. albicans), Trichophyton mentagrophytes (T. mentagrophytes), and Microsporum gypseum (M. gypseum), where compound 6 showed excellent activity against fungi T. mentagrophytes with an MIC value of 12.5 μM. In accordance with the molecular docking study, ecurvoside (1) or pose 472 interacted well with the 3TOP enzyme: PDB and the molecular dynamic simulations proved that the complex of ecurvoside and 3TOP has a stable simulation time of 50-100 ns and the significant residual amino acids in 3TOP are relative to interactions more than one time such as Asp 960, Glu 961, Lys 1088, Glu 1095, Arg 1097, Gly 1102, Thr 1103, Gln 1109, Glu 1178: A chain and Glu 1095, Thr 1101, and Asp 1107: B chain. The docking studies of compounds 1-7 to the enzyme 2VF5 explain the general mechanism to inhibit bacteria and proved that compound 6 (pose 370) inhibited stronger than compound 7 (pose 362) and compound 5 (pose 280), and compounds 1 to 4 do not interact well with 2VF5.
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Affiliation(s)
- Tran Thi Ngoc Mai
- Institute of Applied Sciences, HUTECH University 475A Dien Bien Phu Street, Ward 25, Binh Thanh District Ho Chi Minh City Vietnam
| | - Phan Nhat Minh
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Institute of Chemical Technology, Vietnam Academy of Science and Technology 1A TL29 Street, Thanh Loc Ward, District 12 Ho Chi Minh City Vietnam
| | - Nguyen Tan Phat
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Institute of Chemical Technology, Vietnam Academy of Science and Technology 1A TL29 Street, Thanh Loc Ward, District 12 Ho Chi Minh City Vietnam
| | - Thuc Huy Duong
- Department of Chemistry, Ho Chi Minh City University of Education 280 An Duong Vuong Street, District 5 748342 Ho Chi Minh City Vietnam
| | - Tran Nguyen Minh An
- Faculty of Chemical Engineering, Industrial University of Ho Chi Minh City Ho Chi Minh City 71420 Vietnam
| | - Van Son Dang
- Institute of Applied Sciences, HUTECH University 475A Dien Bien Phu Street, Ward 25, Binh Thanh District Ho Chi Minh City Vietnam
- Institute of Tropical Biology, Vietnam Academy of Science and Technology 85 Tran Quoc Toan Street, District 3 Ho Chi Minh City 700000 Vietnam
| | - Nguyen Van Hue
- University of Agriculture and Forestry, Hue University 52000 Vietnam
| | - Mai Dinh Tri
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
- Institute of Chemical Technology, Vietnam Academy of Science and Technology 1A TL29 Street, Thanh Loc Ward, District 12 Ho Chi Minh City Vietnam
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Kiran KS, Kameshwar VH, Mudnakudu Nagaraju KK, Nagalambika P, Varadaraju KR, Karthik NA, Dugganaboyana GK, Nanjunda Swamy S, Krishna KL, Kumar JR. Diosmin: A Daboia russelii venom PLA 2s inhibitor- purified, and characterized from Oxalis corniculata L medicinal plant. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116977. [PMID: 37544341 DOI: 10.1016/j.jep.2023.116977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Oxalis corniculata L is a medicinal plant that belongs to the Oxalidaceae family. It is a little, slow-growing plant with a frail appearance typically found in mild temperate and tropical areas like Pakistan and India. This plant also includes many other bioactive substances, including alkaloids, flavonoids, terpenoids, cardiac glycosides, saponins, phlobatannins, and steroids. AIM OF THE STUDY To investigate the anti-inflammatory effects of Compound diosmin, which is derived from Oxalis corniculata L, on VRV-PL-5 and VRV-PL-8a isolated from Vipera russelli. MATERIALS AND METHODS Extraction, purification, and characterization of bioactive by TLC, HPTLC, FT-IR analysis, UV-Vis spectrophotometer, LC-MS/MS Analysis, NMR, XRD Analysis, In vitro evaluation, Circular dichroism spectroscopy, in vivo, and in silico studies. RESULTS In this study, the extract of Oxalis corniculata was evaluated for its in vitro and in vivo anti-inflammatory effect against PLA2. The methanolic extract decreased hemolytic activity by about 60% at 1:75 w/w and neutralized the hemolytic activity completely at 1:100 w/w concentration. Diosmin inhibited VRV-PL-5 and VRV-PL-8a in a dose-dependent manner, with the extent of inhibition being about 56% for VRV-PL-5120 μM and VRV-PL-8a by 62% at the same concentration with IC50 concentrations of 87.08 μM for VRV-PL-5 and 82.08 μM for VRV-PL-8a, while at 75 μM. Diosmin inhibited the hemolytic activity of VRV-PL-5 by about 85%, and at the same concentration, VRV-PL-8a inhibited by about 75%. UV-CD spectra at the IC50 concentration of diosmin disrupted the secondary structure of VRV-PL-5 &VRV-PL-8a. In vivo, studies showed decreased myotoxicity and cardiotoxicity of the VRV-PL-5 &VRV-PL-8a, which was seen in the decrease in cytoplasmic markers LDH and CPK levels in the serum when incubated with diosmin. Furthermore, Histopathological studies of Muscles and lungs revealed that diosmin considerably protects against cellular abnormality caused by VRV-PL-5 & VRV-PL-8a. Molecular docking, MM/GBSA, and molecular dynamics simulation studies show that the diosmin is a potent inhibitor for VRV-PL-5 and VRV-PL-8a. CONCLUSION This study shows that diosmin is a potentially effective VRV-PL-5 and VRV-PL-8a.
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Affiliation(s)
- K S Kiran
- Division of Biochemistry, School of Life Science, JSS Academy of Higher Education and Research, Mysore-15, India
| | - Vivek Hamse Kameshwar
- Department of Biochemistry, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B. G. Nagara- 571448, Nagamangala (T), Mandya (D), Karnataka, India; Department of Biotechnology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, B. G. Nagara- 571448, Nagamangala (T), Mandya (D), Karnataka, India
| | | | - Prasad Nagalambika
- Department of Microbiology, School of Life Sciences, JSS Academy of Higher Education and Research, Mysore-15, India
| | - Kavitha Raj Varadaraju
- Division of Biochemistry, School of Life Science, JSS Academy of Higher Education and Research, Mysore-15, India
| | - N Awathade Karthik
- Division of Biochemistry, School of Life Science, JSS Academy of Higher Education and Research, Mysore-15, India
| | - Guru Kumar Dugganaboyana
- Division of Biochemistry, School of Life Science, JSS Academy of Higher Education and Research, Mysore-15, India
| | - S Nanjunda Swamy
- Department of Biotechnology, Sri Jayachamarajendra College of Engineering, JSS Science and Technological University, Mysore, India
| | - K L Krishna
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysore-15, India
| | - J R Kumar
- Division of Biochemistry, School of Life Science, JSS Academy of Higher Education and Research, Mysore-15, India.
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Xi Z, Li L, Liu Z, Wu X, Xu Y, Zhang R. Rational Design of l-Threonine Transaldolase-Mediated System for Enhanced Florfenicol Intermediate Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:461-474. [PMID: 38153324 DOI: 10.1021/acs.jafc.3c05267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
l-threo-p-methylsulfonylphenylserine (compound 1b) is the main intermediate of florfenicol, and its efficient synthesis has been the subject of current research. Herein, Burkholderia diffusa l-threonine transaldolase (BuLTTA) was rationally designed based on the sequence-structure-function relationship. A mutant M4 (Asn35Ser/Thr352Asn) could produce 35.5 mM 1b with 88.8% conversion and 93.8% diastereoselectivity, 314 and 129% of the values observed for wild-type BuLTTA. Molecular dynamics simulations indicated that the shortened distance between key active site residues and the transition state (PLP-1b) and the improved hydrogen bond force enhanced the catalytic performance of the M4 variant. Then, the mutant M4 was combined with K. kurtzmanii alcohol dehydrogenase (KkADH) to eliminate the BuLTTA-inhibiting byproduct acetaldehyde, and a cosubstrate was added to regenerate the ADH cofactor NADH. Under optimized conditions, the yield of 1b reached 115.2 mM with a conversion of 96% and a diastereoselectivity of 95.5%. This work provides a new strategy for the efficient and sustainable production of 1b.
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Affiliation(s)
- Zhiwen Xi
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Lihong Li
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Zhiyong Liu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiaolong Wu
- Department of Infection Control, Affiliated Hospital of Jiangnan University, 214122 Wuxi, P. R. China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Rongzhen Zhang
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
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Bhatt S, Choudhary P, Chatterjee S, Akhter Y. Comparative analysis of SilA-laccase mediated degradation of ciprofloxacin, norfloxacin and ofloxacin and interpretation of the possible catalytic mechanism. J Biomol Struct Dyn 2024; 42:425-434. [PMID: 37096761 DOI: 10.1080/07391102.2023.2197074] [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: 12/09/2022] [Accepted: 03/13/2023] [Indexed: 04/26/2023]
Abstract
Fluoroquinolones (FQs) are the most commonly used antimicrobial drugs and regardless of their advantages in the healthcare sector, the pollution of these antimicrobial drugs in the environment has big concerns about human and environmental health. The presence of these antibiotic drugs even at the lowest concentrations in the environment has resulted in the emergence and spread of antibiotic resistance. Hence, it is necessary to remediate these pollutants from the environment. Previously alkaline laccase (SilA) from Streptomyces ipomoeae has been demonstrated to show degrading potentials against two of the FQs, Ciprofloxacin (CIP) and Norfloxacin (NOR); however, the molecular mechanism was not elucidated in detail. In this study, we have analyzed the possible molecular catalytic mechanism of FQ degrading SilA-laccase for the degradation of the FQs, CIP, NOR and Ofloxacin (OFL) using three-dimensional protein structure modeling, molecular docking and molecular dynamic (MD) studies. The comparative protein sequence analysis revealed the presence of tetrapeptide conserved catalytic motif, His102-X-His104-Gly105. After evaluating the active site of the enzyme in depth using CDD, COACH and S-site tools, we have identified the catalytic triad composed of three conserved amino acid residues, His102, Val103 and Tyr108 with which ligands interacted during the catalysis process. By analyzing the MD trajectories, it is revealed that the highest degradation potential of SilA is for CIP followed by NOR and OFL. Ultimately, this study provides the possible comparative catalytic mechanism for the degradation of CIP, NOR and OFL by the SilA enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunidhi Bhatt
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Distt-Kangara, Himachal Pradesh, India
| | - Priyanka Choudhary
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Distt-Kangara, Himachal Pradesh, India
| | - Subhankar Chatterjee
- Bioremediation and Metabolomics Research Group, Department of Ecology & Environmental Sciences, Pondicherry University, Kalapet, Puducherry, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Antony A, Veerappapillai S, Karuppasamy R. In-silico bioprospecting of secondary metabolites from endophytic Streptomyces spp. against Magnaporthe oryzae, a cereal killer fungus. 3 Biotech 2024; 14:15. [PMID: 38125652 PMCID: PMC10728396 DOI: 10.1007/s13205-023-03859-7] [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: 09/08/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
Rice blast disease, caused by Magnaporthe oryzae, is the most devastating cereal killer worldwide. Note that melanin pigment is an essential factor of M. oryzae virulence, thus fungicides interfering with melanin biosynthesizing enzymes would reduce the pathogenicity. Scytalone dehydratase (SDH) is the key target for commercial fungicides, like carpropamid, due to its role in the dehydration reaction of the fungal melanin pathway. However, a single-point mutation (V75M) in SDH elicits resistance to carpropamid. A lack of effective fungicides against this resistant strain expedited the quest for novel bioactive inhibitors. Currently, bacterial endophytes like Streptomyces have been heralded for synthesizing bioactive metabolites to protect plants from phytopathogens. The literature search led to the identification of 21 Streptomyces spp. symbionts of paddy that can suppress M. oryzae growth. An antiSMASH server was used to explore Streptomyces spp. gene clusters and found 4463 putative metabolites. Besides, 745 unique metabolites were subjected to a series of virtual screening techniques. Ideally, this process identified five potential SDH inhibitors. The docking result highlights that the metabolite pseudopyronine A interacted hydrophobically with both Val75 of SDHWT and Met75 of SDHV75M targets. Moreover, pseudopyronine A has a higher binding free energy with SDHWT (- 89.94 kcal/mol) and SDHV75M (- 71.95 kcal/mol). Interestingly, the pyranones scaffold of pseudopyronine A was reported for antifungal activity against phytopathogens. Dynamic behavior confirms that pseudopyronine A has excellent conformational states with both SDHWT and SDHV75M. Altogether, we hope that this study creates a new avenue for the discovery of novel phytopathogen inhibitors from endophytes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03859-7.
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Affiliation(s)
- Ajitha Antony
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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Dhanalakshmi B, Anil Kumar BM, Muddenahalli Srinivasa S, Vivek HK, Sennappan M, Rangappa S, Srinivasa Murthy V. Design and synthesis of 4-aminophenol-1,3,4-oxadiazole derivative potentiates apoptosis by targeting MAP kinase in triple negative breast cancer cells. J Biomol Struct Dyn 2023:1-16. [PMID: 37948299 DOI: 10.1080/07391102.2023.2274973] [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: 02/08/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023]
Abstract
Women below 40 years greatly suffer from triple negative breast cancers (TNBCs). Compared to other breast cancer cases, the poor prognosis and lower survival rate of TNBC patients make it an alarming task to save the human era from this dreadful disease. Therefore, identifying potential novel leads is urgently required to combat the TNBC. To discover a novel anticancer agent, we synthesized a series of novel 4-aminophenolbenzamide-1,3,4 oxadiazole hybrid analogues (7a-l). The structure of the compounds was confirmed by spectral methods (1H & 13C NMR, IR and MS). All the compounds were subjected to their in-silico and in-vitro antiproliferative studies against the TNBC cell lines MDA-MB-468 and MDA-MB-231. The investigations revealed that 7i has significantly promoted apoptosis against MDA-MB-468 and MDA-MB-231 cells with IC50 values of 16.89 and 19.43 µM, respectively. Molecular docking of 7i, with MAPK has exhibited the highest binding score of -7.10 kcal/mol by interacting with crucial amino acids present at the active sites. Molecular docking is further validated with molecular dynamic studies with simulation for 100 ns, depicting various stable interactions with MAPK. Compound 7i, forms stable H-bonds and π-π stacking with amino acid residues. Molecular dynamic simulation (MDS) reveals that hydrophobic and water bridges were very prominent for 7i to bind, with the amino acid residues in close proximity to the active site of p38 MAPK. The investigations show that the In-vitro antiproliferative study of 7i agreed with the in-silico studies. Collectively, our investigations depict 7i as a potent novel lead for the inhibition of TNBCs by targeting p38 MAPK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Boregowda Dhanalakshmi
- Department of Chemistry, School of Engineering, Dayananda Sagar University, Bengaluru, India
- Department of Chemistry, Rajeev Institute of Technology, Visvesvaraya Technological University, Hassan, India
| | - Belagal Motatis Anil Kumar
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala,India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
| | - Sudhanva Muddenahalli Srinivasa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala,India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
| | - Hamse Kameshwar Vivek
- Department of Biotechnology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala, India
- Department of Biochemistry, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
| | - Madhappan Sennappan
- Department of Chemistry, Dayananda Sagar College of Engineering, Bengaluru, India
| | - Shobith Rangappa
- Department of Molecular Biology, Adichunchanagiri School of Natural Sciences, ACU-CRI, Adichunchanagiri University, BGSIT, Nagamangala,India
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, Nagamangala, India
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11
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Hamouda AF, Felemban S. A Bio-Indicator Pilot Study Screening Selected Heavy Metals in Female Hair, Nails, and Serum from Lifestyle Cosmetic, Canned Food, and Manufactured Drink Choices. Molecules 2023; 28:5582. [PMID: 37513454 PMCID: PMC10386365 DOI: 10.3390/molecules28145582] [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: 07/04/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Lifestyles, genetic predispositions, environmental factors, and geographical regions are considered key factors of heavy metals initiatives related to health issues. Heavy metals enter the body via the environment, daily lifestyle, foods, beverages, cosmetics, and other products. The accumulation of heavy metals in the human body leads to neurological issues, carcinogenesis, failure of multiple organs in the body, and a reduction in sensitivity to treatment. We screened for Cr, Al, Pb, and Cd in selected foods, beverages, and cosmetics products depending on questionnaire outcomes from female volunteers. We also screened for Cr, Al, Pb, and Cd on hair, nails, and serum samples using inductively coupled plasma mass spectrometry (ICP-MS) from the same volunteers, and we analyzed the serum cholinesterase and complete blood picture (CBC). We performed an AutoDock study on Cr, Al, Pb, and Cd as potential ligands. Our results indicate that the most elevated heavy metal in the cosmetic sample was Al. In addition, in the food and beverages samples, it was Pb and Al, respectively. The results of the questionnaire showed that 71 percent of the female volunteers used the studied cosmetics, food, and beverages, which were contaminated with Cr, Al, Pb, and Cd, reflecting the high concentration of Cr, Al, Cd, and Pb in the three different types of biological samples of sera, nails, and hair of the same females, with 29 percent of the female volunteers not using the products in the studied samples. Our results also show an elevated level of cholinesterase in the serum of group 1 that was greater than group 2, and this result was confirmed by AutoDock. Moreover, the negative variation in the CBC result was compared with the reference ranges. Future studies should concentrate on the actions of these heavy metal contaminations and their potential health consequences for various human organs individually.
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Affiliation(s)
- Asmaa Fathi Hamouda
- Department of Biochemistry, Faculty of Science, University of Alexandria, Alexandria 21111, Egypt
| | - Shifa Felemban
- Department of Chemistry, Faculty of Applied Science, University College-Al Leith, University of Umm Al-Qura, Makkah 21955, Saudi Arabia
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12
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Liu R, Wang L, Meng Y, Tian Y, Li F, Lu H. Theoretical and Experimental Studies on Plant Light-Dependent Protochlorophyllide Oxidoreductase as a Novel Target for Searching Potential Herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37467369 DOI: 10.1021/acs.jafc.3c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Herbicide resistance is a prevalent problem that has posed a foremost challenge to crop production worldwide. Light-dependent enzyme NADPH: protochlorophyllide oxidoreductase (LPOR) in plants is a metabolic target that could satisfy this unmet demand. Herein, for the first time, we embarked on proposing a new mode of action of herbicides by performing structure-based virtual screening targeting multiple LPOR binding sites, with the determination of further bioactivity on the lead series. The feasibility of exploiting high selectivity and safety herbicides targeting LPOR was discussed from the perspective of the origin and phylogeny. Besides, we revealed the structural rearrangement and the selection key for NADPH cofactor binding to LPOR. Based on these, multitarget virtual screening was performed and the result identified compounds 2 affording micromolar inhibition, in which the IC50 reached 4.74 μM. Transcriptome analysis revealed that compound 2 induced more genes related to chlorophyll synthesis in Arabidopsis thaliana, especially the LPOR genes. Additionally, we clarified that these compounds binding to the site enhanced the overall stability and local rigidity of the complex systems from molecular dynamics simulation. This study delivers a guideline on how to assess activity-determining features of inhibitors to LPOR and how to translate this knowledge into the design of novel and effective inhibitors against malignant weed that act by targeting LPOR.
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Affiliation(s)
- Ruiyuan Liu
- College of Science, China Agricultural University, Beijing 100193, China
| | - Leng Wang
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yue Meng
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yiyi Tian
- College of Science, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Science, China Agricultural University, Beijing 100193, China
| | - Huizhe Lu
- College of Science, China Agricultural University, Beijing 100193, China
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13
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Bhanot V, Pali S, Panwar J. Understanding the in silico aspects of bacterial catabolic cascade for styrene degradation. Proteins 2023; 91:532-541. [PMID: 36416087 DOI: 10.1002/prot.26447] [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: 06/28/2022] [Revised: 10/31/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022]
Abstract
Styrene is a nonpolar organic compound used in very high volume for the industrial scale production of commercially important polymers such as polystyrene resins as well as copolymers like acrylonitrile butadiene styrene, latex, and rubber. These resins are widely used in the manufacturing of various products including single-use plastics such as disposable cups and containers, protective packaging, heat insulation, and so forth. The large-scale utilization leads to the over-accumulation of styrene waste in the environment causing deleterious health risks including cancer, neurological impairment, dysbiosis of central nervous system, and respiratory problems. To eliminate the accumulating waste. Microbial enzyme-based system represents the most environmental friendly and sustainable approach for elimination of styrene waste. However, comprehensive understanding of the enzyme-substrate interaction and associated pathways would be crucial for developing large-scale disposal systems. This study aims to understand the molecular interaction between the protein-ligand complexes of the styrene catabolic reactions by bacterial enzymes of sty operon. Molecular docking analysis for catalytic enzymes namely, styrene monooxygenase (SMO), styrene oxide isomerase (SOI), and phenylacetaldehyde dehydrogenase (PAD) of the bacterial sty operon was carried out with their individual substrates, that is, styrene, styrene oxide, and phenylacetic acid, respectively. The binding energy, amino acids forming binding cavity, and binding interactions between the protein-ligand binding sites were calculated for each case. The obtained binding energies showed a stable association of these complexes indicating the future scope of their utilization for large-scale bioremediation of styrene, and its commercially used polymers and copolymers.
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Affiliation(s)
- Vishalakshi Bhanot
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Snigdha Pali
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Jitendra Panwar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
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14
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Zamzami MA. Molecular docking, molecular dynamics simulation and MM-GBSA studies of the activity of glycyrrhizin relevant substructures on SARS-CoV-2 RNA-dependent-RNA polymerase. J Biomol Struct Dyn 2023; 41:1846-1858. [PMID: 35037842 DOI: 10.1080/07391102.2021.2025147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
SARS-CoV-2 is the causative agent of Coronavirus Disease (COVID-19), which is a life-threatening disease. The World Health Organization has classified COVID-19 as a severe worldwide public health pandemic due to its high death rate, quick transmission, and lack of medicines. To counteract the recurrence of the severe acute respiratory syndrome, active antiviral medications are urgently required. Glycyrrhizin was documented with activity on different viral proteins, including SARS-CoV-2; in this study, the activity of glycyrrhizin and its substructures (604 molecules) were screened on SARS-CoV-2 RNA-dependent-RNA polymerase using molecular docking, molecular dynamic (MD) simulation, and MM/GBSA. Sixteen molecules exhibited docking energy higher than -7 kcal/mol; four compounds (10772603, 101088272, 154730753 and glycyrrhizin) showed the highest binding energy, and good stability during MD simulation. The glycyrrhizin compound exhibited favorable docking energy (-7.9 kcal/mol), and it was the most stable complex during MD simulation. The predicted binding free energy of the glycyrrhizin complex was -57 ± 8 kcal/mol. These findings suggest that this molecule, after more validation, could become a good candidate for developing and manufacturing an anti-SARS-CoV-2 medication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
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15
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Mansouri N, Benslama O, Arhab R. Homology modeling, docking and molecular dynamics studies of some secondary metabolites of actinomycetes as biocontrol agents against the 3HNR enzyme of the phytopathogenic fungus Alternaria alternata. J Biomol Struct Dyn 2023; 41:871-883. [PMID: 34895071 DOI: 10.1080/07391102.2021.2014970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Early blight of tomatoes is a common disease caused by the phytopathogenic fungi Alternaria, in particular the species A. alternata. This disease causes significant losses in the tomato harvest. The enzyme 1,3,8-trihydroxynaphthalene reductase (3HNR) is a key enzyme involved in the production of melanin, that plays a crucial role in the process of fungi invasion. This enzyme is the target of some chemical fungicides, but the problem of resistance against these molecules requires the search for new molecules that are both effective and environment-friendly. Actinomycetes represent an important source of secondary metabolites with antimicrobial activity. Thus, in this study 110 secondary metabolites of actinomycetes were subjected to an in silico screening of their antifungal activity as possible inhibitors of the 3HNR of A. alternata. For this reason, the 3D structure of this enzyme was modeled. Then, a molecular docking study of the secondary actinomycetal metabolites was carried out within the catalytic site of the enzyme. Indole-3-carboxylic acid, Streptokordin, 3-Phenylpropionic acid, Phenylacetate, and 8-Hydroxyquinoline have shown the most promising results with binding energies of -6.1 kcal/mol, -6.1 kcal/mol, -5.4 kcal/mol, -5.3 kcal/mol, and -5.0 kcal/mol, respectively. These metabolites have also shown satisfactory results for drug-likeness and ADMET analysis. The interaction stability of the Streptokordin, Indole-3-carboxylic acid, Phenylacetate, and 8-Hydroxyquinoline within the catalytic site of 3HNR was confirmed by the results of the MD simulation and MM-PBSA analyzes. With their favorable interactive and pharmacokinetic characteristics, these metabolites may be potential antifungal molecules against A. alternata, and good candidates for further studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nedjwa Mansouri
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, Department of Natural and Life Sciences, Larbi Ben M'Hidi University, Oum El Bouaghi, Algeria
| | - Ouided Benslama
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, Department of Natural and Life Sciences, Larbi Ben M'Hidi University, Oum El Bouaghi, Algeria
| | - Rabah Arhab
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, Department of Natural and Life Sciences, Larbi Ben M'Hidi University, Oum El Bouaghi, Algeria
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16
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Verma AK, Ahmed SF, Hossain MS, Bhojiya AA, Upadhyay SK, Srivastava AK, Singh N, Harina H, Rahaman MM, Bahadur NM. Unlocking SGK1 inhibitor potential of bis-[1-N,7-N, pyrazolo tetraethoxyphthalimido{-4-(3,5-Dimethyl-4-(spiro-3-methylpyazolo)-1,7-dihydro-1H-dipyrazolo[3,4-b;4',3'-e]pyridin-8-yl)}]p-disubstituted phenyl compounds: a computational study. J Biomol Struct Dyn 2022; 40:13412-13431. [PMID: 34696688 DOI: 10.1080/07391102.2021.1988711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SGK1 (Serum and Glucocorticoid Regulated Kinase 1), a serine/threonine kinase that is activated by various stimuli, including serum and glucocorticoids. It controls inflammation, apoptosis, hormone release, neuro-excitability and cell proliferation, all of which play an important role in cancer progression and metastasis. SGK1 was recently proposed as a potential drug target for cancer, diabetes, and neurodegenerative diseases. In this study, molecular docking, physiochemical, toxicological properties and molecular dynamic simulation of the Bis-[1-N,7-N, Pyrazolo tetraethoxyphthalimido{-4-(3,5-Dimethyl-4-(spiro-3-methylpyazolo)-1,7-dihydro-1H-dipyrazolo[3,4-b;4',3'-e]pyridin-8-yl)}]p-disubstituted phenyl compoundsand reference EMD638683 against new SGK1 target protein. Compared to the reference inhibitor EMD638683, we choose the best compounds (series 2-6) based on the binding energy (in the range from -11.0 to -10.6 kcal/mol). With the exception of compounds 2 and 6, none of the compounds posed a risk for AMES toxicity or carcinogenicity due to their toxicological properties. 100 ns MD simulation accompanied by MM/PBSA energy calculations and PCA. According to MD simulation results, the binding of compounds 3, 4 and 5 stabilizes the SGK1 structure and causes febrile conformational changes compared to EMD638683. As a result of this research, the final selected compounds 3, 4 and 5 can be used as scaffolds to develop promising SGK1 inhibitors for the treatment of related diseases such as cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhishek Kumar Verma
- Department of Life Sciences, Faculty of Science and Technology, Mewar University, Gangrar, Chittorgarh, Rajasthan, India
| | - Sk Faisal Ahmed
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Md Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
| | - Ali Asger Bhojiya
- Faculty of Agriculture and Veterinary Sciences, Mewar University, Gangrar, Chittorgarh, Rajasthan, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, Uttar Pradesh, India
| | | | - Nripendra Singh
- Department of Pharmacy, V.B.S, Purvanchal University, Jaunpur, Uttar Pradesh, India
| | - Harina Harina
- Department of Life Sciences, Faculty of Science and Technology, Mewar University, Gangrar, Chittorgarh, Rajasthan, India
| | | | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Sonapur, Noakhali, Bangladesh
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17
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Katari SK, Pasala C, Nalamolu RM, Bitla AR, Umamaheswari A. In silico trials to design potent inhibitors against matrilysin (MMP-7). J Biomol Struct Dyn 2022; 40:11851-11862. [PMID: 34405760 DOI: 10.1080/07391102.2021.1965032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The study deals with structure-based rational drug design against the chief zinc-rely endopeptidase called matrilysin (MMP-7) that is involved in inflammatory and metastasis process of several carcinomas. Hyperactivated matrilysin of human was targeted, because of its hydrolytic actions on extracellular matrix (ECM) protein components constitutes fibrillar collagens, gelatins, fibronectins and it also activates zymogen forms of vital matrix metalloproteinases (gelatinase A-MMP-2 and B-MMP-9) responsible for ECM destruction in many cancers. In the present work, e-pharmacophores were generated for the respective five co-crystal structures of human matrilysin by mapping ligand's pharmacophoric features. During the lead-optimization campaign, the five e-pharmacophores-based shape screening against an in-house library of >21 million compounds created a dataset of 5000 structural analogs. The subsequent three different docking strategies, including rigid-receptor docking, quantum-polarized-ligand docking, induced-fit docking and free energy binding calculations resulted four leads as novel and potent MMP-7 binders. These four leads were observed with good pharmacological features and good receiver operating characteristics curve metrics (ROC: 0.93) in post-docking evaluations against five existing co-crystal inhibitors and 1000 decoy molecules with MMP-7. Moreover, stability and dynamics behavior of matrilysin-lead1 complex and matrilysin-cocrystal ligand (TQJ) complex were analyzed in natural physiological milieu of 1000 ns or 1 µs molecular dynamics simulations. Lead1-MMP-7 complex was found with an average Cα root-mean-square deviation (RMSD) of 2.35 Å, average ligand root-mean-square fluctuations (RMSF) of 0.66 Å and the strong metallic interactions with E220, a key residue for proteolytic action thereby hinders ECM proteolysis that in turn can halt metastatic cancerous condition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sudheer Kumar Katari
- Department of Bioinformatics, Bioinformatics Centre, Sri Venkateswara Institute of Medical Sciences University, Tirupati, Andhra Pradesh, India
| | - Chiranjeevi Pasala
- Department of Bioinformatics, Bioinformatics Centre, Sri Venkateswara Institute of Medical Sciences University, Tirupati, Andhra Pradesh, India
| | - Ravina Madhulitha Nalamolu
- Department of Bioinformatics, Bioinformatics Centre, Sri Venkateswara Institute of Medical Sciences University, Tirupati, Andhra Pradesh, India
| | - Aparna R Bitla
- Department of Biochemistry, Sri Venkateswara Institute of Medical Sciences University, Tirupati, Andhra Pradesh, India
| | - Amineni Umamaheswari
- Department of Bioinformatics, Bioinformatics Centre, Sri Venkateswara Institute of Medical Sciences University, Tirupati, Andhra Pradesh, India
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18
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Computational investigation of natural compounds as potential main protease (M pro) inhibitors for SARS-CoV-2 virus. Comput Biol Med 2022; 151:106318. [PMID: 36423529 PMCID: PMC9673090 DOI: 10.1016/j.compbiomed.2022.106318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 11/05/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is significantly impacting human lives, overburdening the healthcare system and weakening global economies. Plant-derived natural compounds are being largely tested for their efficacy against COVID-19 targets to combat SARS-CoV-2 infection. The SARS-CoV-2 Main protease (Mpro) is considered an appealing target because of its role in replication in host cells. We curated a set of 7809 natural compounds by combining the collections of five databases viz Dr Duke's Phytochemical and Ethnobotanical database, IMPPAT, PhytoHub, AromaDb and Zinc. We applied a rigorous computational approach to identify lead molecules from our curated compound set using docking, dynamic simulations, the free energy of binding and DFT calculations. Theaflavin and ginkgetin have emerged as better molecules with a similar inhibition profile in both SARS-CoV-2 and Omicron variants.
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19
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Sharma N, Gupta N, Orfali R, Kumar V, Patel CN, Peng J, Perveen S. Evaluation of the Antifungal, Antioxidant, and Anti-Diabetic Potential of the Essential Oil of Curcuma longa Leaves from the North-Western Himalayas by In Vitro and In Silico Analysis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227664. [PMID: 36431765 PMCID: PMC9695312 DOI: 10.3390/molecules27227664] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Essential oils (EOs) have gained immense popularity due to considerable interest in the health, food, and pharmaceutical industries. The present study aimed to evaluate the antimicrobial and antioxidant activity and the anti-diabetic potential of Curcuma longa leaf (CLO) essential oil. Further, major phytocompounds of CLO were analyzed for their in-silico interactions with antifungal, antioxidant, and anti-diabetic proteins. CLO was found to have a strong antifungal activity against the tested Candida species with zone of inhibition (ZOI)-11.5 ± 0.71 mm to 13 ± 1.41 mm and minimum inhibitory concentration (MIC) was 0.63%. CLO also showed antioxidant activity, with IC50 values of 5.85 ± 1.61 µg/mL using 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging assay and 32.92 ± 0.64 µM using ferric reducing antioxidant power (FRAP) assay. CLO also showed anti-diabetic activity with an IC50 of 43.06 ± 1.24 µg/mL as compared to metformin (half maximal inhibitory concentration, IC50-16.503 ± 0.66 µg/mL). Gas chromatography-mass spectrometry (GC-MS) analysis of CLO showed the presence of (-)-zingiberene (17.84%); 3,7-cyclodecadien-1-one, 3,7-dimethyl-10-(1-methylethylidene)-(15.31%); cyclohexene, 4-methyl-3-(1-methylethylidene) (12.47%); and (+)-4-Carene (11.89%) as major phytocompounds. Molecular docking of these compounds with antifungal proteins (cytochrome P450 14 alpha-sterol demethylase, PDB ID: 1EA1, and N-myristoyl transferase, PDB ID: 1IYL), antioxidant (human peroxiredoxin 5, PDB ID: 1HD2), and anti-diabetic proteins (human pancreatic alpha-amylase, PDB ID: 1HNY) showed strong binding of 3,7-cyclodecadien-1-one with all the selected protein targets. Furthermore, molecular dynamics (MD) simulations for a 100 ns time scale revealed that most of the key contacts of target proteins were retained throughout the simulation trajectories. Binding free energy calculations using molecular mechanics generalized born surface area (MM/GBSA), and drug-likeness and toxicity analysis also proved the potential for 3,7-cyclodecadien-1-one, 3,7-dimethyl-10-(1-methylethylidene) to replace toxic synthetic drugs and act as natural antioxidants.
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Affiliation(s)
- Nitin Sharma
- Department of Biotechnology, Chandigarh College of Technology, CGC, Landran, Mohali 140307, India
- Correspondence: (N.S.); (S.P.)
| | - Nidhi Gupta
- Department of Biotechnology, Chandigarh College of Technology, CGC, Landran, Mohali 140307, India
| | - Raha Orfali
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11495, Saudi Arabia
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, India
| | - Chirag N. Patel
- Department of Botany, Bioinformatics, and Climatic Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad 380009, India
| | - Jiangnan Peng
- Department of Medicinal, School of Computer, Mathematical and Natural Sciences, Morgan State University, Baltimore, MD 21251, USA
| | - Shagufta Perveen
- Department of Medicinal, School of Computer, Mathematical and Natural Sciences, Morgan State University, Baltimore, MD 21251, USA
- Correspondence: (N.S.); (S.P.)
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20
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Targeting aurora kinase a (AURKA) in cancer: molecular docking and dynamic simulations of potential AURKA inhibitors. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:246. [PMID: 36180808 DOI: 10.1007/s12032-022-01852-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
The Aurora family of serine/threonine kinases in mammals are key regulators of mitotic progression and are commonly upregulated in human tumors. Since AURKA's increased expression has been linked to cancer, AURKA inhibitors could reduce AURKA expression and function as potent therapeutic drugs. The study's objective was to find and categorize inhibitors with a stronger affinity for AURKA. This study also aimed to identify AURKA's expression profile and prognostic significance across pan-cancers. We looked into therapeutic compounds that were structurally comparable to MK8745 for their potential to selectively inhibit AURKA. We used drug likeliness analysis, MD simulation studies to evaluate the therapeutic possibility of screened MK8745 analogues. AURKA was found to be strongly upregulated in several cancers and is linked to worse overall and relapse-free survival. The Molecular docking and dynamic analysis revealed two new MK8745 analogues to be potent AURKA inhibitors with higher binding affinities and stabilities than MK8745. Furthermore, MK8745 analogues are potential replacements for MK8745 because they have strong binding affinity, which is consistent with MDS results, and have appropriate ADMET properties. Through basic, clinical, and preclinical research, the identification of novel compounds may open the door for their prospective use in the prevention of cancer.
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Alshehri B. Expression patterns and therapeutic implications of histone deacetylase-1 across carcinomas: a comprehensive molecular docking and MD simulation study. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:209. [PMID: 36175584 DOI: 10.1007/s12032-022-01811-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/26/2022] [Indexed: 11/29/2022]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that control the expression of genes by deacetylating lysine residues on histone and nonhistone proteins. They control the expression of several proteins linked to the development and spread of cancer. Deregulation of HDAC1 has been reported across several tumors, and targeting HDAC1 with specific inhibitors has demonstrated a promising therapeutic strategy. Mocetinostat, an HDAC1 inhibitor, is yielding promising results both in vitro and in vivo studies. However, toxicities associated with Mocetinostat limit its therapeutic efficacy, so there is an urgent need to investigate novel HDAC1 inhibitors. The present study aimed to explore novel HDAC1 inhibitors and investigate the expression profile, and the prognostic and diagnostic significance of HDAC1 across pan-cancers. HDAC1 was found overexpressed across several tumors and its high expression signifies worse OS and RFS. Also, the study identified two novel HDAC1 inhibitors using an in-silico approach with high binding affinity for HDAC1 compared to Mocetinostat and formed significantly stable complexes. In conclusion, the study signifies that targeting HDAC1 is a promising therapeutic strategy, and exploring novel therapeutic agents through basic, translational design may lead to their ultimate use in cancer prevention.
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Affiliation(s)
- Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Almajmaah, 11952, Kingdom of Saudi Arabia.
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22
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Joshi M, Purohit M, Shah DP, Patel D, Depani P, Moryani P, Krishnakumar A. Pathogenomic in silico approach identifies NSP-A and Fe-IIISBP as possible drug targets in Neisseria Meningitidis MC58 and development of pharmacophores as novel therapeutic candidates. Mol Divers 2022:10.1007/s11030-022-10480-y. [PMID: 35879631 DOI: 10.1007/s11030-022-10480-y] [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: 04/13/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Meningitis creates a life-threatening clinical crisis. Moreover, the administered antibiotics result into multi-drug resistance, thereby necessitating development of alternative therapeutic strategies. This study aimed at identifying novel-drug targets in Neisseria meningitidis and therapeutic molecules which can be exploited for the treatment of meningitis. Novel targets were identified by applying a pathogenomic approach involving protein data-set mining, subtractive channel analysis and subsequent qualitative analysis comprising of in silico pharmacokinetics, molecular docking and pharmacophore generation. Pathogenomic studies revealed Neisserial Surface Protein A (NSP-A) and Iron-III-Substrate Binding Protein (Fe-IIISBP) as potential targets. Two pharmacophore models comprising of 2-(biaryl) carbapenems, efavirenz, praziquantel and pyrimethamine for NSP-A and 2-(biaryl) carbapenems, trimipramine and pyrimethamine for Fe-IIISBP, showed successful docking, followed drug-likeness criteria and generated pharmacophore model with a score of 8.08 and 8.818, respectively, which had further been docked to the target stably. Thus, our study identifies NSP-A and Fe-IIISBP as novel targets in Neisseria meningitidis for which 2-(biaryl) carbapenems, efavirenz, praziquantel, trimipramine and pyrimethamine may be employed for effective treatment of meningitis.
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Affiliation(s)
- Madhavi Joshi
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India
| | - Maitree Purohit
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India
| | - Dhriti P Shah
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India
| | - Devanshi Patel
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India
| | - Preksha Depani
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India
| | - Premkumar Moryani
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India
| | - Amee Krishnakumar
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat, 382 481, India.
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23
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Sreenatha V, Srinivasa SM, Rajendra Prasad K. Design, Synthesis, Bioevaluation, DFT, Docking, and Molecular Dynamic Simulation for Selected Novel 1,3,4-Oxadiazole - Indole Derivatives Hybrid against Estrogen Receptor alpha. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Sofi S, Mehraj U, Qayoom H, Aisha S, Almilaibary A, Alkhanani M, Mir MA. Targeting cyclin-dependent kinase 1 (CDK1) in cancer: molecular docking and dynamic simulations of potential CDK1 inhibitors. Med Oncol 2022; 39:133. [PMID: 35723742 PMCID: PMC9207877 DOI: 10.1007/s12032-022-01748-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Cell cycle dysregulation is a characteristic hallmark of malignancies, which results in uncontrolled cell proliferation and eventual tumor formation. Cyclin-dependent kinase 1 (CDK1) is a member of the family of cell cycle regulatory proteins involved in cell cycle maintenance. Given that overexpression of CDK1 has been associated with cancer, CDK1 inhibitors may restore equilibrium to the skewed cell cycle system and operate as an effective therapeutic drug. This study aimed to identify and classify inhibitors having a higher affinity for CDK1 and also evaluate the expression pattern and prognostic relevance of CDK1 in a wide range of cancers. We investigated therapeutic molecules structurally similar to dinaciclib for their ability to inhibit CDK1 selectively. To assess the therapeutic potential of screened Dinaciclib analogs, we used drug likeliness analysis, molecular docking, and simulation analysis. CDK1 was found to be highly upregulated across several malignancies and is associated with poor overall and relapse-free survival. Molecular docking and dynamics evaluation identified two novel dinaciclib analogs as potent CDK1 inhibitors with high binding affinity and stability compared to dinaciclib. The results indicate that increased CDK1 expression is associated with decreased OS and RFS. Additionally, dinaciclib analogs are prospective replacements for dinaciclib since they exhibit increased binding affinity, consistent with MDS findings, and have acceptable ADMET qualities. The discovery of new compounds may pave the road for their future application in cancer prevention through basic, preclinical, and clinical research.
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Affiliation(s)
- Shazia Sofi
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Umar Mehraj
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Hina Qayoom
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Shariqa Aisha
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Abdullah Almilaibary
- Department of Family and Community Medicine, Albaha University, Albaha, 65511, Kingdom of Saudi Arabia
| | - Mustfa Alkhanani
- Emergency Service Department, College of Applied Science, AlMaarefa University, Riyadh, 13713, Kingdom of Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India.
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25
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Thermostable Chitosan-L-Asparaginase conjugate from Aspergillus fumigatus is a novel structurally stable composite for abolishing acrylamide formation in French fried potatoes. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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Mugaranja KP, Kulal A. Investigation of effective natural inhibitors for starch hydrolysing enzymes from Simaroubaceae plants by molecular docking analysis and comparison with in-vitro studies. Heliyon 2022; 8:e09360. [PMID: 35600433 PMCID: PMC9118686 DOI: 10.1016/j.heliyon.2022.e09360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/22/2021] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
The present study aims to find the effective natural enzyme inhibitors against alpha-amylase and alpha-glucosidase from the array of compounds identified in plants of the Simaroubaceae family using molecular docking and ADME/Toxicity studies. Among the 218 compounds docked against seven enzymes, buddlenol-A and citrusin-B showed the best binding energies (kcal/mol) of -7.830 and -7.383 against human salivary alpha-amylase and pancreatic alpha-amylase respectively. The other two compounds 9-hydroxycanthin-6-one and bruceolline-B had the best binding energy of -6.461 and -7.576 against N-terminal and C-terminal maltase glucoamylase respectively. Whereas the binding energy of prosopine (-6.499) and fisetinidol (-7.575) was considered as the best against N-terminal and C-terminal sucrase-isomaltase respectively. Picrasidine-X showed the best binding energy (-7.592) against yeast alpha-glucosidase. The study revealed that the seven compounds which showed the best binding energy against respective enzymes are considered as the ‘lead hit compounds’. Even though the ‘lead hit compounds’ are not obeying all the laws of ADMET, the drug-likeness properties of 9-hydroxycanthin-6-one, fisetinidol, picrasidine-X, and prosopine were considerable. Also, kaempferol-3-O-pentoside was the recent compound identified from the Simarouba glauca plant extract found to be one among the top five lead hit compounds against four enzymes. This study provides valuable insight into the direction of developing natural compounds as potential starch hydrolysing enzyme inhibitors for managing type 2 diabetes.
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α-Glucosidase Inhibitory and Antimicrobial Benzoylphloroglucinols from Garcinia schomburgakiana Fruits: In Vitro and In Silico Studies. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082574. [PMID: 35458771 PMCID: PMC9032663 DOI: 10.3390/molecules27082574] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/17/2022]
Abstract
α-Glucosidase plays a role in hydrolyzing complex carbohydrates into glucose, which is easily absorbed, causing postprandial hyperglycemia. Inhibition of α-glucosidase is therefore an ideal approach to preventing this condition. A novel polyprenylated benzoylphloroglucinol, which we named schomburgkianone I (1), was isolated from the fruit of Garcinia schomburgkiana, along with an already-reported compound, guttiferone K (2). The structures of the two compounds were determined using NMR and HRESIMS analysis, and comparisons were made with previous studies. Compounds 1 and 2 exhibited potent α-glucosidase inhibition (IC50s of 21.2 and 34.8 µM, respectively), outperforming the acarbose positive control. Compound 1 produced wide zones of inhibition against Staphylococcus aureus and Enterococcus faecium (of 21 and 20 mm, respectively), compared with the 19 and 20 mm zones of compound 2, at a concentration of 50 µg/mL. The MIC value of compound 1 against S. aureus was 13.32 µM. An in silico molecular docking model suggested that both compounds are potent inhibitors of enzyme α-glucosidase and are therefore leading candidates as therapies for diabetes mellitus.
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28
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M PH, Al-Ostoot FH, Vivek HK, Khanum SA. Synthesis, characterization, DFT, docking studies and molecular dynamics of some 3-phenyl-5-furan isoxazole derivatives as anti-inflammatory and anti-ulcer agents. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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29
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Patel CN, Goswami D, Jaiswal DG, Jani SP, Parmar RM, Rawal RM, Pandya HA. Excavating phytochemicals from plants possessing antiviral activities for identifying SARS-CoV hemagglutinin-esterase inhibitors by diligent computational workflow. J Biomol Struct Dyn 2022; 41:2382-2397. [PMID: 35098887 DOI: 10.1080/07391102.2022.2033642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coronaviruses (CoVs) belong to a group of RNA viruses that cause diseases in vertebrates including. Newer and deadlier than SARS CoV-2 are sought to appear in future for which the scientific community must be prepared with the strategies for their control. Spike protein (S-protein) of all the CoVs require angiotensin-converting enzyme2 (ACE2), while CoVs also require hemagglutinin-acetylesterase (HE) glycoprotein receptor to simultaneously interact with O-acetylated sialic acids on host cells, both these interactions enable viral particle to enter host cell leading to its infection. Target inhibition of viral S-protein and HE glycoprotein receptor can lead to a development of therapy against the SARS CoV-2. The proposition is to recognize molecules from the bundle of phytochemicals of medicinal plants known to possess antiviral potentials as a lead that could interact and mask the active site of, HE glycoprotein which would ideally bind to O-acetylated sialic acids on human host cells. Such molecules can be addressed as 'HE glycoprotein blockers'. A library of 110 phytochemicals from Withania somnifera, Asparagus racemosus, Zinziber officinalis, Allium sativum, Curcuma longa and Adhatoda vasica was constructed and was used under present study. In silico analysis was employed with plant-derived phytochemicals. The molecular docking, molecular dynamics simulations over the scale of 1000 ns (1 μs) and ADMET prediction revealed that the Withania somnifera (ashwagandha) and Asparagus racemosus (shatavari) plants possessed various steroidal saponins and alkaloids which could potentially inhibit the COVID-19 virus and even other CoVs targeted HE glycoprotein receptor.
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Affiliation(s)
- Chirag N Patel
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dharmesh G Jaiswal
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Siddhi P Jani
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Robin M Parmar
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh M Rawal
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Himanshu A Pandya
- Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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30
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Jabir NR, Rehman MT, Alsolami K, Shakil S, Zughaibi TA, Alserihi RF, Khan MS, AlAjmi MF, Tabrez S. Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer's treatment. Ann Med 2021; 53:2332-2344. [PMID: 34889159 PMCID: PMC8667905 DOI: 10.1080/07853890.2021.2009124] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments. AIMS As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and γ-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and γ-secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and γ-secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA). RESULTS The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of -7.0 to -10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≤-8 kcal/mol against BACE-1 and γ-secretase. For the selected enzyme targets, BACE-1 and γ-secretase, 6Z5 displayed the lowest binding energy of -10.1 and -9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and γ-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes. CONCLUSION The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and γ-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies.
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Affiliation(s)
- Nasimudeen R. Jabir
- Department of Biochemistry, Centre for Research and Development, PRIST University, Thanjavur, India
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Khadeejah Alsolami
- Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Shazi Shakil
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Torki A. Zughaibi
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed F. Alserihi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- 3D Bioprinting Unit, Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd. Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Aamir M, Karmakar P, Singh VK, Kashyap SP, Pandey S, Singh BK, Singh PM, Singh J. A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). PHYSIOLOGIA PLANTARUM 2021; 173:1729-1764. [PMID: 33547804 DOI: 10.1111/ppl.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.
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Affiliation(s)
- Mohd Aamir
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Pradip Karmakar
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Sudhakar Pandey
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Binod Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Jagdish Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
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32
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Hui Z, Dong QQ, Shu HP, Tu YC, Liao QQ, Yao LJ. Mechanistic insights into the renoprotective role of curcumin in cisplatin-induced acute kidney injury: network pharmacology analysis and experimental validation. Bioengineered 2021; 12:11041-11056. [PMID: 34802380 PMCID: PMC8810021 DOI: 10.1080/21655979.2021.2005916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cisplatin-induced acute kidney injury (CP-AKI) is a severe complication in patients receiving CP chemotherapy. However, effective therapies for CP-AKI are currently lacking. Curcumin (CUR), a natural polyphenol, is extracted from the rhizome of turmeric and has been reported to have nephroprotective activity. However, the role of CUR in CP-AKI remains unclear. This study aimed to explore the mechanism of CUR in CP-AKI by combining a network pharmacology approach with experimental validations. The analysis revealed 176 potential targets of CUR based on the HERB database and 1,286 related targets of CP-AKI from the GeneCards, DrugBank, and OMIM databases. Further, 106 common targets of CUR against CP-AKI were obtained, and these common targets constructed a protein-protein interaction (PPI) network. In addition, the core targets were screened from the PPI network using Cytoscape. Molecular docking revealed that CUR displayed the best binding to AKT1. Gene Ontology (GO) analysis indicated that the primary biological processes of CUR against CP-AKI included cellular response to chemical stress and apoptotic regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested that the PI3K-Akt signaling pathway was most significantly enriched in CUR against CP-AKI. Western blotting and flow cytometry showed that CUR inhibited apoptosis induced by CP by activating the Akt signaling pathway in human kidney tubular epithelial cells (HK-2). Altogether, our findings demonstrated that CUR alleviated apoptosis by activating the Akt signaling pathway in CP-AKI in vitro. These data provide a scientific basis for future investigations into the clinical application of CUR against CP-AKI.
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Affiliation(s)
- Zhang Hui
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing-Qing Dong
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua-Pan Shu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu-Chi Tu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian-Qian Liao
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Jun Yao
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Swapnil P, Meena M, Rai AK. Molecular interaction of nitrate transporter proteins with recombinant glycinebetaine results in efficient nitrate uptake in the cyanobacterium Anabaena PCC 7120. PLoS One 2021; 16:e0257870. [PMID: 34793479 PMCID: PMC8601584 DOI: 10.1371/journal.pone.0257870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/14/2021] [Indexed: 11/18/2022] Open
Abstract
Nitrate transport in cyanobacteria is mediated by ABC-transporter, which consists of a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). Under salt stress, recombinant glycinebetaine (GB) not only protected the rate of nitrate transport in transgenic Anabaena PCC 7120, rather stimulated the rate by interacting with the ABC-transporter proteins. In silico analyses revealed that nrtA protein consisted of 427 amino acids, the majority of which were hydrophobic and contained a Tat (twin-arginine translocation) signal profile of 34 amino acids (1-34). The nrtC subunit of 657 amino acids contained two hydrophobic distinct domains; the N-terminal (5-228 amino acids), which was 59% identical to nrtD (the ATP-binding subunit) and the C-terminal (268-591), 28.2% identical to nrtA, suggesting C-terminal as a solute binding domain and N-terminal as ATP binding domain. Subunit nrtD consisted of 277 amino acids and its N-terminal (21-254) was an ATP binding motif. Phylogenetic analysis revealed that nitrate-ABC-transporter proteins are highly conserved among the cyanobacterial species, though variation existed in sequences resulting in several subclades. Nostoc PCC 7120 was very close to Anabaena variabilis ATCC 29413, Anabaena sp. 4-3 and Anabaena sp. CA = ATCC 33047. On the other, Nostoc spp. NIES-3756 and PCC 7524 were often found in the same subclade suggesting more work before referring it to Anabaena PCC 7120 or Nostoc PCC 7120. The molecular interaction of nitrate with nrtA was hydrophilic, while hydrophobic with nrtC and nrtD. GB interaction with nrtACD was hydrophobic and showed higher affinity compared to nitrate.
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Affiliation(s)
- Prashant Swapnil
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
- Department of Botany, University of Delhi, New Delhi, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Ashwani K. Rai
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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Swapnil P, Meena M, Rai AK. Molecular interaction of nitrate transporter proteins with recombinant glycinebetaine results in efficient nitrate uptake in the cyanobacterium Anabaena PCC 7120. PLoS One 2021; 16:e0257870. [DOI: https:/doi.org/10.1371/journal.pone.0257870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023] Open
Abstract
Nitrate transport in cyanobacteria is mediated by ABC-transporter, which consists of a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). Under salt stress, recombinant glycinebetaine (GB) not only protected the rate of nitrate transport in transgenic Anabaena PCC 7120, rather stimulated the rate by interacting with the ABC-transporter proteins. In silico analyses revealed that nrtA protein consisted of 427 amino acids, the majority of which were hydrophobic and contained a Tat (twin-arginine translocation) signal profile of 34 amino acids (1–34). The nrtC subunit of 657 amino acids contained two hydrophobic distinct domains; the N-terminal (5–228 amino acids), which was 59% identical to nrtD (the ATP-binding subunit) and the C-terminal (268–591), 28.2% identical to nrtA, suggesting C-terminal as a solute binding domain and N-terminal as ATP binding domain. Subunit nrtD consisted of 277 amino acids and its N-terminal (21–254) was an ATP binding motif. Phylogenetic analysis revealed that nitrate-ABC-transporter proteins are highly conserved among the cyanobacterial species, though variation existed in sequences resulting in several subclades. Nostoc PCC 7120 was very close to Anabaena variabilis ATCC 29413, Anabaena sp. 4–3 and Anabaena sp. CA = ATCC 33047. On the other, Nostoc spp. NIES-3756 and PCC 7524 were often found in the same subclade suggesting more work before referring it to Anabaena PCC 7120 or Nostoc PCC 7120. The molecular interaction of nitrate with nrtA was hydrophilic, while hydrophobic with nrtC and nrtD. GB interaction with nrtACD was hydrophobic and showed higher affinity compared to nitrate.
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Shreevatsa B, Dharmashekara C, Swamy VH, Gowda MV, Achar RR, Kameshwar VH, Thimmulappa RK, Syed A, Elgorban AM, Al-Rejaie SS, Ortega-Castro J, Frau J, Flores-Holguín N, Shivamallu C, Kollur SP, Glossman-Mitnik D. Virtual Screening for Potential Phytobioactives as Therapeutic Leads to Inhibit NQO1 for Selective Anticancer Therapy. Molecules 2021; 26:molecules26226863. [PMID: 34833955 PMCID: PMC8622762 DOI: 10.3390/molecules26226863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022] Open
Abstract
NAD(P)H:quinone acceptor oxidoreductase-1 (NQO1) is a ubiquitous flavin adenine dinucleotide-dependent flavoprotein that promotes obligatory two-electron reductions of quinones, quinonimines, nitroaromatics, and azo dyes. NQO1 is a multifunctional antioxidant enzyme whose expression and deletion are linked to reduced and increased oxidative stress susceptibilities. NQO1 acts as both a tumor suppressor and tumor promoter; thus, the inhibition of NQO1 results in less tumor burden. In addition, the high expression of NQO1 is associated with a shorter survival time of cancer patients. Inhibiting NQO1 also enables certain anticancer agents to evade the detoxification process. In this study, a series of phytobioactives were screened based on their chemical classes such as coumarins, flavonoids, and triterpenoids for their action on NQO1. The in silico evaluations were conducted using PyRx virtual screening tools, where the flavone compound, Orientin showed a better binding affinity score of −8.18 when compared with standard inhibitor Dicumarol with favorable ADME properties. An MD simulation study found that the Orientin binding to NQO1 away from the substrate-binding site induces a potential conformational change in the substrate-binding site, thereby inhibiting substrate accessibility towards the FAD-binding domain. Furthermore, with this computational approach we are offering a scope for validation of the new therapeutic components for their in vitro and in vivo efficacy against NQO1.
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Affiliation(s)
- Bhargav Shreevatsa
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
| | - Chandan Dharmashekara
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
| | - Vikas Halasumane Swamy
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
| | - Meghana V. Gowda
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Vivek Hamse Kameshwar
- School of Natural Science, Adichunchanagiri University, B.G. Nagara, Nagamangala, Mandya 571448, India;
| | - Rajesh Kumar Thimmulappa
- Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India;
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Salim S. Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh 11451, Saudi Arabia;
| | - Joaquín Ortega-Castro
- Departament de Química, Universitat de les Illes Balears, 07122 Palma de Malllorca, Spain; (J.O.-C.); (J.F.)
| | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, 07122 Palma de Malllorca, Spain; (J.O.-C.); (J.F.)
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Shiva Prasad Kollur
- Department of Sciences, Mysuru Campus, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru 570026, India
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
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Suryakoppa KS, Kameshwar VH, Appadurai R, Eranna S, Khan MHM. Enantiomeric Separation of Indole-3-Propanamide Derivatives by Using Supercritical Fluid Chromatography on a Polysaccharide-Based Chiral Stationary Phase. J Chromatogr Sci 2021; 60:692-704. [PMID: 34510190 DOI: 10.1093/chromsci/bmab102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/28/2021] [Accepted: 08/06/2021] [Indexed: 11/14/2022]
Abstract
Thirteen pairs of I3P enantiomers were screened using nine polysaccharide chiral stationary phases and three different mobile phases. The purification strategy for 13 pairs of I3P enantiomers were designed and optimized considering enantiomeric purity and enrichment of isomers. Out of 13 I3P derivatives which were screened using supercritical fluid chromatography, 10 derivatives displayed excellent baseline separation using a Lux Cellulose-4 column and their resolution from higher to lower order of I3P-11, 13, 4, 12, 2, 1, 9, 3, 7 and 8 derivatives whereas in case of Lux Cellulose-2 column, the moderate separation was achieved as compared to Cellulose-4 in the order I3P-5, 6 and 10 derivatives. Excellent enantiomeric separations and retentions for all 13 I3P enantiomer derivatives were obtained in Cellulose-4 and Cellulose-2 columns in presences of methanol as organic modifier without any additives except in the case of I3P 12 enantiomer. The absolute stereochemical assignment of the purified isomers was determined through an optical rotation study. Among the series of I3P derivatives, I3P-5 showed potent antioxidant activity against catalase with an IC50 value of 13.78 μM. Further molecular docking, MM/GBSA and molecular dynamics studies revealed that the I3P-5 derivatives effectively bind to catalase with a docking score of -5.41 kcal/mol. Which validated chiral docking and indicated great potential for enantiomeric separation in drug discovery and present studies (R)-enantiomer preferentially depicts good binding capacity with catalase.
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Affiliation(s)
- Kaveesha Srinivasa Suryakoppa
- Discovery Chemistry-Analytical Research and Development, Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Estate - Phase-IV, Bommasandra-Jigani Link Road, Bengaluru 560 099, Karnataka, India.,Department of Chemistry, Jawaharlal Nehru National College of Engineering, Visvesvaraya Technological University, Shimoga 577204, Karnataka, India
| | - Vivek Hamse Kameshwar
- School of Natural Science, Adichunchanagiri University-Center for Research and Innovation, BGSIT campus, Adichunchanagiri University, B. G Nagara, 571448 Mandya, Karnataka, India
| | - Ramesh Appadurai
- Discovery Chemistry-Analytical Research and Development, Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Estate - Phase-IV, Bommasandra-Jigani Link Road, Bengaluru 560 099, Karnataka, India
| | - Siddalingamurthy Eranna
- Research and Development, Synus lab LLP, R23, Bommasandra industrial area, Jigani Link Road, Bengaluru 560099, Karnataka, India
| | - M H Moinuddin Khan
- Department of Chemistry, Jawaharlal Nehru National College of Engineering, Visvesvaraya Technological University, Shimoga 577204, Karnataka, India
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Jabir NR, Rehman MT, Tabrez S, Alserihi RF, AlAjmi MF, Khan MS, Husain FM, Ahmed BA. Identification of Butyrylcholinesterase and Monoamine Oxidase B Targeted Ligands and their Putative Application in Alzheimer's Treatment: A Computational Strategy. Curr Pharm Des 2021; 27:2425-2434. [PMID: 33634754 DOI: 10.2174/1381612827666210226123240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND With the burgeoning worldwide aging population, the incidence of Alzheimer's disease (AD) and its associated disorders is continuously rising. To appraise other relevant drug targets that could lead to potent enzyme targeting, 13 previously predicted ligands (shown favorable binding with AChE (acetylcholinesterase) and GSK-3 (glycogen synthase kinase) were screened for targeting 3 different enzymes, namely butyrylcholinesterase (BChE), monoamine oxidase A (MAO-A), and monoamine oxidase B (MAO-B) to possibly meet the unmet medical need of better AD treatment. MATERIALS AND METHODS The study utilized in silico screening of 13 ligands against BChE, MAO-A and MAOB using PyRx-Python prescription 0.8. The visualization of the active interaction of studied compounds with targeted proteins was performed by Discovery Studio 2020 (BIOVIA). RESULTS The computational screening of studied ligands revealed the docking energies in the range of -2.4 to -11.3 kcal/mol for all the studied enzymes. Among the 13 ligands, 8 ligands (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed the binding energies of ≤ -8.0 kcal/mol towards BChE, MAO-A and MAO-B. The ligand 6Z5 was found to be the most potent inhibitor of BChE and MAO-B, with a binding energy of -9.7 and -10.4 kcal mol, respectively. Molecular dynamics simulation of BChE-6Z5 and MAO-B-6Z5 complex confirmed the formation of a stable complex. CONCLUSION Our computational screening, molecular docking, and molecular dynamics simulation studies revealed that the above-mentioned enzymes targeted ligands might expedite the future design of potent anti-AD drugs generated on this chemical scaffold.
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Affiliation(s)
- Nasimudeen R Jabir
- Department of Biochemistry, Centre for Research and Development, PRIST University, Vallam, Thanjavur, Tamil Nadu, India
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed F Alserihi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair, Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Bakrudeen Ali Ahmed
- Department of Biochemistry, Centre for Research and Development, PRIST University, Vallam, Thanjavur, Tamil Nadu, India
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The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain. Int J Biol Macromol 2021; 186:54-70. [PMID: 34237360 DOI: 10.1016/j.ijbiomac.2021.06.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/20/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022]
Abstract
Lactoferrin (Lf), a bioactive milk protein, exhibits strong anticancer and antifungal activities. The search for Lf targets and mechanisms of action is of utmost importance to enhance its effective applications. A common feature among Lf-treated cancer and fungal cells is the inhibition of a proton pump called V-ATPase. Lf-driven V-ATPase inhibition leads to cytosolic acidification, ultimately causing cell death of cancer and fungal cells. Given that a detailed elucidation of how Lf and V-ATPase interact is still missing, herein we aimed to fill this gap by employing a five-stage computational approach. Molecular dynamics simulations of both proteins were performed to obtain a robust sampling of their conformational landscape, followed by clustering, which allowed retrieving representative structures, to then perform protein-protein docking. Subsequently, molecular dynamics simulations of the docked complexes and free binding energy calculations were carried out to evaluate the dynamic binding process and build a final ranking based on the binding affinities. Detailed atomist analysis of the top ranked complexes clearly indicates that Lf binds to the V1 cytosolic domain of V-ATPase. Particularly, our data suggest that Lf binds to the interfaces between A/B subunits, where the ATP hydrolysis occurs, thus inhibiting this process. The free energy decomposition analysis further identified key binding residues that will certainly aid in the rational design of follow-up experimental studies, hence bridging computational and experimental biochemistry.
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Manibalan S, Harison Raj AB, Achary A. Screening of Atherosclerotic Druggable Targets from the Proteome Network of Differentially Expressed Genes. Assay Drug Dev Technol 2021; 19:290-299. [PMID: 34171974 DOI: 10.1089/adt.2021.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Differently expressed genes of atherosclerotic sample analysis are helpful to sort the prominent genes that influence the plaque formation and progression. Scientific evidence-based protein-protein interaction network (PPIN) studies were used to find hub proteins in complex disease conditions. Druggable capacity is one of the important parameters to confirm as a successful drug target. Construction of protein interaction network and principal node analysis (PNA) on atherosclerotic data sets lead to screen the hub proteins. Furthermore, druggable property of protein pocket confirms the targetability of susceptible target candidates and for target selection. Differentially expressed genes are identified through GEO2R analyzer on data sets of various atherosclerotic samples. STRING database and Cytoscape are employed to construct PPIN. Targets were identified by PNA such as centrality measures and clustering algorithm. Gene Ontology enrichment also used as one of the screening parameters to filter the candidates related to atherosclerotic terms. Topological evaluation of target protein was successfully done by ITASSER and GROMACS, respectively. Grid-based principle of DoGSiteScorer is utilized for druggability analysis. Six proteins such as integrin alpha L (ITGAL), metallothionein 1F (MT1F), metallothionein 1X (MT1X), P-selectin glycoprotein ligand-1 (SELPLG), solute carrier family 30 A, zinc transporter protein (SLC30A1), and TNFSF13B are screened as potential biomarkers through network-based analysis. Among the six, ITGAL, SELPLG, SLC30A1, and TNSF13B are identified as better prioritized atherosclerotic targets through druggability efficiency.
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Affiliation(s)
- Subramaniyan Manibalan
- Centre for Research, Department of Biotechnology, Kamaraj College of Engineering and Technology, Madurai, India
| | | | - Anant Achary
- Centre for Research, Department of Biotechnology, Kamaraj College of Engineering and Technology, Madurai, India
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40
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Santacruz-Juárez E, Buendia-Corona RE, Ramírez RE, Sánchez C. Fungal enzymes for the degradation of polyethylene: Molecular docking simulation and biodegradation pathway proposal. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125118. [PMID: 33485228 DOI: 10.1016/j.jhazmat.2021.125118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/17/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Polyethylene (PE) is one of the most highly consumed petroleum-based polymers and its accumulation as waste causes environmental pollution. In this sense, the use of microorganisms and their enzymes represents the most ecofriendly and effective decontamination approach. In this work, molecular docking simulation for catalytic enzyme degradation of PE was carried out using individual enzymes: laccase (Lac), manganese peroxidase (MnP), lignin peroxidase (LiP) and unspecific peroxygenase (UnP). PE-binding energy, PE-binding affinity and dimensions of PE-binding sites in the enzyme cavity were calculated in each case. Four hypothetical PE biodegradation pathways were proposed using individual enzymes, and one pathway was proposed using a synergic enzyme combination. These results show that in nature, enzymes act in a synergic manner, using their specific features to undertake an extraordinarily effective sequential catalytic process for organopollutants degradation. In this process, Lac (oxidase) is crucial to provide hydrogen peroxide to the medium to ensure pollutant breakdown. UnP is a versatile enzyme that offers a promising practical application for the degradation of PE and other pollutants due to its cavity features. This is the first in silico report of PE enzymatic degradation, showing the mode of interaction of PE with enzymes as well as the degradation mechanism.
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Affiliation(s)
- Ericka Santacruz-Juárez
- Universidad Politécnica de Tlaxcala. San Pedro Xalcatzinco, Tepeyanco, Tlaxcala C. P. 90180, Mexico
| | - Ricardo E Buendia-Corona
- Departamento de Fisicomatemáticas, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y 14 Sur, Col. San Manuel, C.P. 72570, Puebla, Pue., Mexico
| | - Ramsés E Ramírez
- Departamento de Fisicomatemáticas, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y 14 Sur, Col. San Manuel, C.P. 72570, Puebla, Pue., Mexico
| | - Carmen Sánchez
- Laboratory of Biotechnology, Research Centre for Biological Sciences, Universidad Autónoma de Tlaxcala, Ixtacuixtla, Tlaxcala C.P. 90120, Mexico.
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Li Q, Hu S, Huang L, Zhang J, Cao G. Evaluating the Therapeutic Mechanisms of Selected Active Compounds in Cornus Officinalis and Paeonia Lactiflora in Rheumatoid Arthritis via Network Pharmacology Analysis. Front Pharmacol 2021; 12:648037. [PMID: 33967784 PMCID: PMC8097135 DOI: 10.3389/fphar.2021.648037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/18/2021] [Indexed: 11/18/2022] Open
Abstract
Cornus officinalis Sieb et. Zucc and Paeonia lactiflora Pall. have exhibited favorable therapeutic effects against rheumatoid arthritis (RA), but the specific mechanisms of their active compounds remain unclear. The aim of this study was to comprehensively analyze the therapeutic mechanisms of selected active compounds in Cornus officinalis (loganin, ursolic acid, and morroniside) and Paeonia lactiflora (paeoniflorin and albiflorin) via network pharmacology. The pharmacological properties of the five active compounds were evaluated and their potential target genes were identified by database screening. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional analysis were performed to determine the enriched molecular pathways associated with the active compounds. Using network pharmacology tools, eight genes (IL1β, VEGFA, STAT3, TP53, IL6, TNF, FOS, and LGALS3) were identified as common targets between RA and the five active compounds. Molecular docking simulation revealed the compound-target relationship between the five active compounds and three selected targets from the eight common ones (LGALS3, STAT3, and VEGFA). The compound-target relationships were subsequently validated via preliminary in vivo experiments in a rat model of collagen-induced arthritis. Rats subjected to collagen-induced arthritis showed increased protein expression of LGALS3, STAT3, and VEGFA in synovial tissues. However, treatment using Cornus officinalis or/and Paeonia lactiflora, as well as their most drug-like active compounds (ursolic acid or/and paeoniflorin, respectively, identified based on pharmacological properties), attenuated the expression of these three targets, as previously predicted. Collectively, network pharmacology allowed the pharmacological and molecular roles of Cornus officinalis and Paeonia lactiflora to be systematically revealed, further establishing them as important candidate drugs in the treatment and management of RA.
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Affiliation(s)
- Qinglin Li
- Scientific Research Department, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shaoqi Hu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Lichuang Huang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jida Zhang
- Institute of Basic Research in Clinical Medicine, College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Gang Cao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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Sharma PP, Kumar S, Kaushik K, Singh A, Singh IK, Grishina M, Pandey KC, Singh P, Potemkin V, Poonam, Singh G, Rathi B. In silico validation of novel inhibitors of malarial aspartyl protease, plasmepsin V and antimalarial efficacy prediction. J Biomol Struct Dyn 2021; 40:8352-8364. [PMID: 33870856 DOI: 10.1080/07391102.2021.1911855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Plasmepsin V (Plm V) is an essential aspartic protease required for survival of the malaria parasite, Plasmodium falciparum (Pf). Plm V is required for cleaving the PEXEL motifs of many Pf proteins and its inhibition leads to a knockout effect, indicating its suitability as potential drug target. To decipher new inhibitors of PfPlm V, molecular docking of four HIV-1 protease inhibitors active against PfPlmV was performed on Glide module of Schrödinger suite that supported saquinavir as a lead drug, and therefore, selected as a control. Saquinavir contains an important hydroxyethylamine (HEA) pharmacophore, which was utilized as backbone coupled with piperazine scaffold to build new library of compounds. Newly designed HEA compounds were screened virtually against Plm V. Molecular docking led to a few hits (1 and 3) with higher docking score over the control drug. Notably, compound 1 showed the highest docking score (-11.90 kcal/mol) and XP Gscore (-11.948 kcal/mol). The Prime MMGBSA binding free energy for compound 1 (-60.88 kcal/mol) and 3 (-50.96 kcal/mol) was higher than saquinavir (-37.51 kcal/mol). The binding free energy for the last frame of molecular dynamic simulation supported compound 1 (-92.88 kcal/mol) as potent inhibitor of PfPlm V over saquinavir (-72.77 kcal/mol), and thus, deserves experimental validations in culture and subsequently in animal models.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prem Prakash Sharma
- Department of Biomedical Engineering, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat, Haryana, India.,Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Sumit Kumar
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Kumar Kaushik
- Centre for Fire, Explosives & Environment Safety, Fire Chemistry Group, Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Lab., Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
| | - Kailash C Pandey
- Host-Parasite Interaction Biology Group, National Institute of Malaria Research, New Delhi, India
| | | | - Vladimir Potemkin
- Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Geeta Singh
- Department of Biomedical Engineering, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat, Haryana, India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India.,Laboratory of Computational Modelling of Drugs, South Ural State University, Russia
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Paramashivam S, Balasubramaniam S, Dhiraviam KN. Computational exploration of vicine - an alkaloid glycoside mediated pathological hallmark of adenosine kinase to promote neurological disorder. Metab Brain Dis 2021; 36:653-667. [PMID: 33496919 DOI: 10.1007/s11011-021-00674-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
Epilepsy disease is characterized by the neuronal dysfunction or abnormal neuronal activity of the brain which is regulated by astrocytes. These are glial cells and found to be the major regulators of the brain which are guided by the occurrence of adenosine kinase (ADK) enzyme in the central nervous system (CNS). During the normal physiological environment, ADK maintains the level of adenosine in the CNS. Dysfunction of ADK levels results in accumulation of adenosine levels in the CNS that leads to the pathophysiology of the brain such as astrogliosis which is a pathological hallmark of epileptic seizures. Vicine, an alkaloid glycoside in bitter gourd juice (Momordica charantia) is found to be toxic to the human system if the bitter gourd juice is consumed more. This compound inhibits ADK enzyme activity to lead epilepsy and seizure. Here, the toxic effect of vicine targeting ADK using computational predictions was investigated. The 3-dimensional structure of ADK has been constructed using I-Tasser, which has been refined by ModRefiner, GalaxyRefine, and 3D refine and it was endorsed using PROCHECK, ERRAT, and VADAR. 3D structure of the ligand molecule has been obtained from PubChem. Molecular docking has been achieved using AutoDock 4.2 software, from which the outcome showed the effective interaction between vicine and ADK, which attains binding free energy (∆G) of - 4.13 kcal/mol. Vicine molecule interacts with the active region ARG 149 of ADK and inhibits the functions of ADK that may cause imbalance in energy homeostasis. Also, pre-ADMET results robustly propose in which vicine possesses toxicity, and meanwhile, from the Ames test, it was shown as mutagenic. Hence, the results from our study suggest that vicine was shown to be toxic that suppresses the ADK activity to undergo pathological conditions in the neuronal junctions to lead epilepsy.
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Affiliation(s)
- SathishKumar Paramashivam
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamilnadu, 625021, India
| | | | - Kannan Narayanan Dhiraviam
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamilnadu, 625021, India.
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Sarkar B, Alam S, Rajib TK, Islam SS, Araf Y, Ullah MA. Identification of the most potent acetylcholinesterase inhibitors from plants for possible treatment of Alzheimer’s disease: a computational approach. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-020-00127-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Being one of the rapidly growing dementia type diseases in the world, Alzheimer’s disease (AD) has gained much attention from researchers in the recent decades. Many hypotheses have been developed that describe different reasons for the development of AD. Among them, the cholinergic hypothesis depicts that the degradation of an important neurotransmitter, acetylcholine by the enzyme acetylcholinesterase (AChE), is responsible for the development of AD. Although, many anti-AChE drugs are already available in the market, their performance sometimes yields unexpected results. For this reason, research works are going on to find out potential anti-AChE agents both from natural and synthetic sources. In this study, 50 potential anti-AChE phytochemicals were analyzed using numerous tools of bioinformatics and in silico biology to find out the best possible anti-AChE agents among the selected 50 ligands through molecular docking, determination of the druglikeness properties, conducting the ADMET test, PASS and P450 site of metabolism prediction, and DFT calculations.
Result
The predictions of this study suggested that among the selected 50 ligands, bellidifolin, naringenin, apigenin, and coptisine were the 4 best compounds with quite similar and sound performance in most of the experiments.
Conclusion
In this study, bellidifolin, naringenin, apigenin, and coptisine were found to be the most effective agents for treating the AD targeting AChE. However, more in vivo and in vitro analyses are required to finally confirm the outcomes of this research.
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Ternikar SG, Patil MB, Pasha I, Khanal P. Gene set enrichment analysis of α-amylase and α-glucosidase inhibitors of Cassia glauca. J Diabetes Metab Disord 2021; 19:683-689. [PMID: 33520796 DOI: 10.1007/s40200-020-00538-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/29/2020] [Indexed: 11/25/2022]
Abstract
Background The present study aimed to evaluate in vitro α-amylase and α-glucosidase inhibitory activity of various extracts of Cassia glauca, predict the binding affinity of multiple phytoconstituents with both enzymes via in silico molecular docking and identify the probably modulated pathways by the lead hit. Methods Different extracts of Cassia glauca i.e. acetone, ethanol, and aqueous extracts were evaluated for α-amylase and α-glucosidase inhibitory activity using in vitro method in which starch and 4-Nitrophenyl β-D-glucopyranoside were used as substrate respectively. Similarly, the docking study was performed using autodock4 to predict the binding affinity of phytoconstituents with α-amylase and α-glucosidase. After docking, ten different poses were obtained for the ligand molecule. Among them, the pose of ligand molecule with the lowest binding energy was visualized in Discovery Studio 2019. Results and conclusion Among the multiple extracts, the aqueous extract showed the highest α-amylase (IC50:652.10 ± 20.09) and α-glucosidase (IC50:482.46 ± 8.70) inhibitory activity. Similarly, cassiaoccidentalin B was predicted to have the highest binding affinity with both enzymes. The potency of aqueous extract to inhibit α-amylase and α-glucosidase could be due to multiple water-soluble compounds like saponins, flavonoids, and glycosides.
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Affiliation(s)
- Shama G Ternikar
- Sant Gajanan Maharaj College of Pharmacy Mahagaon, Maharashtra, India
| | - M B Patil
- Department of Pharmacognosy and Phytochemistry, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010 India
| | - Ismail Pasha
- Department of Pharmacology, Orotta College of Medicine and Health Sciences, Asmara University, Asmara, Eritrea
| | - Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010 India
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Sharma D, Kumar N, Mehrotra T, Pervaiz N, Agrawal L, Tripathi S, Jha A, Poullikkas T, Kumar R, Ledwani L. In vitro and in silico molecular docking studies of Rheum emodi-derived diamagnetic SnO 2 nanoparticles and their cytotoxic effects against breast cancer. NEW J CHEM 2021. [DOI: 10.1039/d0nj04670a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Green-route-bioengineered nanoparticles have received significant attention for diagnosis and treatment of cancer in the medical technology era due to their non-toxic nature, cost-friendliness, and energy efficiency.
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Affiliation(s)
| | - Naveen Kumar
- Department of Physics, Shri Guru Gobind Singh College
- Chandigarh
- India
| | - Tarang Mehrotra
- College of Professional Studies
- Northeastern University
- Boston
- USA
| | | | - Lokesh Agrawal
- Universidad Integral del Caribe y América Latina, Kaminda Cas Grandi #79
- Curaçao
- Molecular Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University
- Okinawa 904-0412
- Japan
| | - Shalini Tripathi
- Department of Material Science
- University of Connecticut
- Storrs
- USA
| | - Abhishek Jha
- Department of Life Sciences
- School of Sciences
- Indira Gandhi National Open University
- India
| | - Thanasis Poullikkas
- Human Biology, School of Integrative and Global Majors, University of Tsukuba
- 1-1-1 Tennodai
- Japan
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba
- 2-1-1 Tennodai
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Prabhavathi H, Dasegowda KR, Renukananda KH, Karunakar P, Lingaraju K, Raja Naika H. Molecular docking and dynamic simulation to identify potential phytocompound inhibitors for EGFR and HER2 as anti-breast cancer agents. J Biomol Struct Dyn 2020; 40:4713-4724. [PMID: 33345701 DOI: 10.1080/07391102.2020.1861982] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Breast cancer is the most prevalent cancer in women worldwide. To treat human breast cancer by inhibiting EGFR and HER2 targets is an important therapeutic option. Phytochemicals are found to have beneficial health effects in treating various diseases. An effort has been made to virtually screen phytochemical inhibitor by molecular docking and dynamic simulation in the current studies. The docking scores analysis resulted in a common hit Panaxadiol ligand with a low dock score for EGFR and HER2 targets. The inhibitory action of the phytocompounds was also validated by comparing it with the reference compounds Erlotinib for EGFR and Neratinib for HER2. Molecular dynamic simulation of EGFR and HER2 lead complexes ensure the ligand's appropriate refinement in the dynamic system. The target and ligand complex interaction motif established a high affinity of lead candidates in a dynamic system similar to molecular docking results. This study reveals that Panaxadiol hit molecule can be developed as a novel multi-target EGFR and HER2 target inhibitor with greater potential and low toxicity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- H Prabhavathi
- Department of Studies & Research in Biotechnology, Tumkur University, Tumakuru, Karnataka, India
| | - K R Dasegowda
- Department of Biotechnology & Genetics, Ramaiah College of Arts, Science and Commerce, Bangalore, Karnataka, India
| | - K H Renukananda
- Department of Mechanical Engineering, RV Institute of Technology and Management, Bangalore, Karnataka, India
| | | | - K Lingaraju
- Department of Studies & Research in Biotechnology, Tumkur University, Tumakuru, Karnataka, India
| | - H Raja Naika
- Department of Studies & Research in Biotechnology, Tumkur University, Tumakuru, Karnataka, India
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Chandrashekar S, Vijayakumar R, Chelliah R, Oh DH. Identification and Purification of Potential Bioactive Peptide of Moringa oleifera Seed Extracts. PLANTS 2020; 9:plants9111445. [PMID: 33120901 PMCID: PMC7716235 DOI: 10.3390/plants9111445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022]
Abstract
The aim of the study was to investigate the antibacterial and anticoagulant activity of Moringa (Moringa oleifera) seed extracts and coagulant protein for their potential application in water treatment. Pathogenic microorganisms were obtained from Ramachandra Hospital, Chennai, India. Bacterial cell aggregation and growth kinetics studies were employed for six bacterial strains with different concentrations of seed extracts and coagulant protein. Moringa seed extract and coagulant protein showed cell aggregation against six bacterial strains, whereas seed extract alone showed growth inhibition of all six bacterial strains for up to 6 h, compared to that of control. Escherichia coli and Salmonella para typhi B did not develop resistance against coagulant protein. The results imply that Moringa oleifera is likely an efficient low-molecular bioactive peptide (with <7.5 kDa plant-based coagulant and antimicrobial peptides, confirmed by applying amino acid sequences), using liquid chromatography–mass spectrometry and HPLC, with the corresponding sequences from Napin-1A peptide posing different degrees of antibacterial activity against different pathogenic organisms.
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Affiliation(s)
- Sangeeta Chandrashekar
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea;
- Department of Physiology, Bharath Institute of Higher Education and Research, Chennai 600 073, India
| | - Raman Vijayakumar
- Department of Physiology, Bharath Institute of Higher Education and Research, Chennai 600 073, India
- Correspondence: (R.V.); (R.C.); (D.-H.O.); Tel.: +82-33-250-6457 (D.-H.O.)
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea;
- Correspondence: (R.V.); (R.C.); (D.-H.O.); Tel.: +82-33-250-6457 (D.-H.O.)
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Korea;
- Correspondence: (R.V.); (R.C.); (D.-H.O.); Tel.: +82-33-250-6457 (D.-H.O.)
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Rahman M, Browne JJ, Van Crugten J, Hasan MF, Liu L, Barkla BJ. In Silico, Molecular Docking and In Vitro Antimicrobial Activity of the Major Rapeseed Seed Storage Proteins. Front Pharmacol 2020; 11:1340. [PMID: 33013372 PMCID: PMC7508056 DOI: 10.3389/fphar.2020.01340] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In addition to their use as an edible oil and condiment crop, mustard and rapeseed (Brassica napus L., B. juncea (L.) Czern., B. nigra (L.) W.D.J.Koch, B. rapa L. and Sinapis alba L.) have been commonly used in traditional medicine for relieving pain, coughs and treating infections. The seeds contain high amounts of oil, while the remaining by-product meal after oil extraction, about 40% of seed dry weight, has a low value despite its high protein-content (~85%). The seed storage proteins (SSP) 2S albumin-type napin and 12S globulin-type cruciferin are the two predominant proteins in the seeds and show potential for value adding to the waste stream; however, information on their biological activities is scarce. In this study, purified napin and cruciferin were tested using in silico, molecular docking, and in vitro approaches for their bioactivity as antimicrobial peptides. MATERIALS AND METHODS The 3D-structure of 2S albumin and 12S globulin storage proteins from B. napus were investigated to predict antimicrobial activity employing an antimicrobial peptide database survey. To gain deeper insights into the potential antimicrobial activity of these SSP, in silico molecular docking was performed. The purified B. napus cruciferin and napin were then tested against both Gram-positive and Gram-negative bacteria for in vitro antimicrobial activity by disc diffusion and microdilution antimicrobial susceptibility testing. RESULTS In silico analysis demonstrated both SSP share similar 3D-structure with other well studied antimicrobial proteins. Molecular docking revealed that the proteins exhibited high binding energy to bacterial enzymes. Cruciferin and napin proteins appeared as a double triplet and a single doublet, respectively, following SDS-PAGE. SDS-PAGE and Western blotting also confirmed the purity of the protein samples used for assessment of antimicrobial activity. Antimicrobial susceptibility testing provided strong evidence for antimicrobial activity for the purified napin protein; however, cruciferin showed no antimicrobial activity, even at the highest dose applied. DISCUSSION In silico and molecular docking results presented evidence for the potential antimicrobial activity of rapeseed cruciferin and napin SSP. However, only the in vitro antimicrobial activity of napin was confirmed. These findings warrant further investigation of this SSP protein as a potential new agent against infectious disease.
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Affiliation(s)
- Mahmudur Rahman
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Jessica J. Browne
- School of Health and Human Sciences, Southern Cross University, Bilinga, QLD, Australia
| | - Jacoba Van Crugten
- School of Health and Human Sciences, Southern Cross University, Bilinga, QLD, Australia
| | | | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Bronwyn J. Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
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Sarkar B, Ullah MA, Islam SS, Rahman MH, Araf Y. Analysis of plant-derived phytochemicals as anti-cancer agents targeting cyclin dependent kinase-2, human topoisomerase IIa and vascular endothelial growth factor receptor-2. J Recept Signal Transduct Res 2020; 41:217-233. [PMID: 32787531 DOI: 10.1080/10799893.2020.1805628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer is caused by a variety of pathways, involving numerous types of enzymes. Among them three enzymes i.e. Cyclin-dependent kinase-2 (CDK-2), Human topoisomerase IIα, and Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) are three of the most common enzymes that are involved in the cancer development. Although many chemical drugs are already available in the market for cancer treatment, plant sources are known to contain a wide variety of agents that are proved to possess potential anticancer activity. In this experiment, total thirty phytochemicals were analyzed against the mentioned three enzymes using different tools of bioinformatics and in silico biology like molecular docking study, drug likeness property experiment, ADME/T test, PASS prediction, and P450 site of metabolism prediction as well as DFT calculation to determine the three best ligands among them that have the capability to inhibit the mentioned enzymes. From the experiment, Epigallocatechin gallate was found to be the best ligand to inhibit CDK-2, Daidzein showed the best inhibitory activities towards the Human topoisomerase IIα, and Quercetin was predicted to be the best agent against VEGFR-2. They were also predicted to be quite safe and effective agents to treat cancer. However, more in vivo and in vitro analyses are required to finally confirm their safety and efficacy in this regard.
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Affiliation(s)
- Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Syed Sajidul Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Hasanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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