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Roth S, Niese R, Müller M, Hall M. Redox Out of the Box: Catalytic Versatility Across NAD(P)H-Dependent Oxidoreductases. Angew Chem Int Ed Engl 2024; 63:e202314740. [PMID: 37924279 DOI: 10.1002/anie.202314740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
The asymmetric reduction of double bonds using NAD(P)H-dependent oxidoreductases has proven to be an efficient tool for the synthesis of important chiral molecules in research and on industrial scale. These enzymes are commercially available in screening kits for the reduction of C=O (ketones), C=C (activated alkenes), or C=N bonds (imines). Recent reports, however, indicate that the ability to accommodate multiple reductase activities on distinct C=X bonds occurs in different enzyme classes, either natively or after mutagenesis. This challenges the common perception of highly selective oxidoreductases for one type of electrophilic substrate. Consideration of this underexplored potential in enzyme screenings and protein engineering campaigns may contribute to the identification of complementary biocatalytic processes for the synthesis of chiral compounds. This review will contribute to a global understanding of the promiscuous behavior of NAD(P)H-dependent oxidoreductases on C=X bond reduction and inspire future discoveries with respect to unconventional biocatalytic routes in asymmetric synthesis.
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Affiliation(s)
- Sebastian Roth
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Richard Niese
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Mélanie Hall
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- BioHealth, Field of Excellence, University of Graz, 8010, Graz, Austria
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2
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Surekha S, Lamiyan AK, Gupta V. Antibiotic Resistant Biofilms and the Quest for Novel Therapeutic Strategies. Indian J Microbiol 2024; 64:20-35. [PMID: 38468748 PMCID: PMC10924852 DOI: 10.1007/s12088-023-01138-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/03/2023] [Indexed: 03/13/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the major leading causes of death around the globe. Present treatment pipelines are insufficient to overcome the critical situation. Prominent biofilm forming human pathogens which can thrive in infection sites using adaptive features results in biofilm persistence. Considering the present scenario, prudential investigations into the mechanisms of resistance target them to improve antibiotic efficacy is required. Regarding this, developing newer and effective treatment options using edge cutting technologies in medical research is the need of time. The reasons underlying the adaptive features in biofilm persistence have been centred on different metabolic and physiological aspects. The high tolerance levels against antibiotics direct researchers to search for novel bioactive molecules that can help combat the problem. In view of this, the present review outlines the focuses on an opportunity of different strategies which are in testing pipeline can thus be developed into products ready to use.
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Affiliation(s)
- Saumya Surekha
- Department of Biochemistry, Panjab University, Chandigarh, India
| | | | - Varsha Gupta
- GMCH: Government Medical College and Hospital, Chandigarh, India
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3
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Zheng J, You J, Zhang D, Zhang X, Chen F, Yang T, Xu M, Hu Y, Rao Z. Pre-optimization and one-step preparation of cascade enzymes system with broad substrates by model guidance: Application of chiral L-norvaline and L-phenylglycine biosynthesis. Bioresour Technol 2024; 393:130125. [PMID: 38040317 DOI: 10.1016/j.biortech.2023.130125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Cascade biocatalyst systems with catalytic promiscuity can be used for synthesis of a class of chiral chemicals but the optimization of these systems by model guidance is poorly explored. In this study, a cascade system with broad substrate spectrum was characterized and simulated by kinetic model with substrates of DL-Norvaline (DL-Nor) and DL-Phenylglycine (DL-Phg) as examples. To evaluate the optimal cascade system, maximum accumulation of intermediate products and conversion rate in the process were investigated by simultaneous solution of the rate equations for varying enzyme quantities. According to the simulation results, the cascade system was optimized by regulating the expression of D-amino acid oxidase and formate dehydrogenase and was prepared by one-step. The conversion efficiency of DL-Nor and DL-Phg have been significantly improved compared with that of before optimization. Moreover, the total of L-Nor and L-Phg were reached 498.2 mM and 79.5 mM through a gradient fed-batch conversion strategy, respectively.
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Affiliation(s)
- Junxian Zheng
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, Fujian, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Danfeng Zhang
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, Fujian, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Fan Chen
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, Fujian, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Yuanqing Hu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, Fujian, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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4
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Pandya VK, Shankar SS, Sonwane BP, Rajesh S, Rathore R, Kumaran S, Kulkarni MJ. Mechanistic insights on anserine hydrolyzing activities of human carnosinases. Biochim Biophys Acta Gen Subj 2023; 1867:130290. [PMID: 36529243 DOI: 10.1016/j.bbagen.2022.130290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 11/16/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Anserine and carnosine represent histidine-containing dipeptides that exert a pluripotent protective effect on human physiology. Anserine is known to protect against oxidative stress in diabetes and cardiovascular diseases. Human carnosinases (CN1 and CN2) are dipeptidases involved in the homeostasis of carnosine. In poikilothermic vertebrates, the anserinase enzyme is responsible for hydrolyzing anserine. However, there is no specific anserine hydrolyzing enzyme present in humans. In this study, we have systematically investigated the anserine hydrolyzing activity of human CN1 and CN2. A targeted multiple reaction monitoring (MRM) based approach was employed for studying the enzyme kinetics of CN1 and CN2 using carnosine and anserine as substrates. Surprisingly, both CN1 and CN2 can hydrolyze anserine effectively. The observed catalytic turnover rate (Vmax/[E]t) was 21.6 s-1 and 2.8 s-1 for CN1 and CN2, respectively. CN1 is almost eight-fold more efficient in hydrolyzing anserine compared to CN2, which is comparable to the efficiency of the carnosine hydrolyzing activity of CN2. The Michaelis constant (Km) value for CN1 (1.96 mM) is almost three-fold lower compared to CN2 (6.33 mM), representing higher substrate affinity for anserine-CN1 interactions. Molecular docking studies showed that anserine binds at the catalytic site of the carnosinases with an affinity similar to carnosine. Overall, the present study elucidated the inherent promiscuity of human carnosinases in hydrolyzing anserine using a sensitive LC-MS/MS approach.
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Affiliation(s)
- Vaibhav Kumar Pandya
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - S Shiva Shankar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Babasaheb P Sonwane
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - S Rajesh
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Rajeshwari Rathore
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sangaralingam Kumaran
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mahesh J Kulkarni
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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5
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Garay J, Csiszár V, Móri TF. Subsistence of sib altruism in different mating systems and Haldane's arithmetic. J Theor Biol 2023; 557:111330. [PMID: 36279958 DOI: 10.1016/j.jtbi.2022.111330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
The moral rule "Risk your life to save your family members" is, at the same time, a biological phenomenon. The prominent population geneticist, J.B.S. Haldane told his friends that he would risk his life to save two drowning brothers, but not one - so the story goes. In biological terms, Haldane's arithmetic claims that sib altruism is evolutionarily rational, whenever by "self-sacrifice" an altruistic gene "rescues", on average, more than one copy of itself in its lineage. Here, we derive conditions for evolutionary stability of sib altruism, using population genetic models for three mating systems (monogamy, promiscuity and polygyny) with linear and non-linear group effect on the siblings' survival rate. We show that for all considered selection situations, the condition of evolutionary stability is equivalent to Haldane's arithmetic. The condition for evolutionary stability is formulated in terms of genetic relatedness and the group effect on the survival probability, similarly to the classical Hamilton's rule. We can set up a "scale of mating systems", since in pairwise interactions the chance of evolutionary stability of sib altruism decreases in this order: monogamy, polygyny and promiscuity. Practice of marrying and siblings' solidarity are moral rules in a secular world and in various religious traditions. These moral rules are not evolutionarily independent, in the sense that the subsistence of sib altruism is more likely in a monogamous population.
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Affiliation(s)
- József Garay
- Centre for Ecological Research, Institute of Evolution, Konkoly-Thege M. út, 29-33, H-1121 Budapest, Hungary; MTA-ELTE Research Group in Theoretical Biology and Evolutionary Ecology and Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter s. 1/C, H-1117 Budapest, Hungary.
| | - Villő Csiszár
- Department of Probability Theory and Statistics, Eötvös Loránd University, Pázmány Péter s. 1/C, H-1117 Budapest, Hungary.
| | - Tamás F Móri
- Alfréd Rényi Institute of Mathematics, Reáltanoda u. 13-15, H-1085 Budapest, Hungary.
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6
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Su H, Sun J, Jia Z, Zhao H, Mao X. Insights into promiscuous chitosanases: the known and the unknown. Appl Microbiol Biotechnol 2022; 106:6887-6898. [PMID: 36178516 DOI: 10.1007/s00253-022-12198-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022]
Abstract
Chitosanase, a glycoside hydrolase (GH), catalyzes the cleavage of β-1,4-glycosidic bonds in polysaccharides and is widely distributed in nature. Many organisms produce chitosanases, and numerous chitosanases in the GH families have been intensely studied. The reported chitosanases mainly cleaved the inter-glucosamine glycosidic bonds, while substrate specificity is not strictly unique due to the existence of bifunctional or multifunctional activity profiles. The promiscuity of chitosanases is essential for the different pathways of biomass polysaccharide conversion and understanding of the chitosanase evolutionary process. However, the reviews for this aspect are completely unknown. This review provides an overview of the promiscuous activities, also considering the substrate and product specificity of chitosanases observed to date. These contribute to important implications for the future discovery and research of promiscuous chitosanases and applications related to biomass conversion. KEY POINTS: • The promiscuity of chitosanases is reviewed for the first time. • The current review provides insights into the substrate specificity of chitosanases. • The mode-product relationship and prospect of promiscuous chitosanases are highlighted.
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Affiliation(s)
- Haipeng Su
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Zhenrong Jia
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Hongjun Zhao
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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7
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Tripathi A, Dutta Dubey K. Combined MD and QM/MM Calculations Reveal Allostery-Driven Promiscuity in Dipeptide Epimerases of Enolase Family. Chem Asian J 2022; 17:e202200528. [PMID: 35722826 DOI: 10.1002/asia.202200528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Indexed: 11/10/2022]
Abstract
The adaptability of the active site to amplify the secondary function is supposed to be the fundamental cause of the promiscuity and the evolution of new functions in enzymes. In most cases, mutations occur close to the active site and/or in the catalytic site to change the active site plasticity to accommodate the non-native substrate. In the present study, using MD simulations and hybrid QM/MM calculations, we have shown a way to enhance the promiscuity, i. e., the allostery-driven promiscuity. Using a case study of the AEE enzyme where the capping loop recognizes the substrate, herein, we show that a single site mutation (D321G) far from the capping loop can induce a large conformational change in the capping loop to recognize different substrates for different functions. The QM/MM calculations for the WT and mutated enzyme provide a first validation of the mechanism of 1,1-proton transfer and dehydration by the AEE enzyme. Since AEE epimerase possesses a highly conserved TIM-barrel fold, we believe that our study provides a crucial lead to understanding the mechanism of emergence of secondary function which can be useful to repurpose ancient enzymes for modern usage.
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Affiliation(s)
- Ankita Tripathi
- Department of Chemistry, School of Natural Science, Shiv Nadar University Delhi-NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh, 201314, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar University Delhi-NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh, 201314, India.,Center for Informatics, Department of Chemistry, School of Natural Science, Shiv Nadar University Delhi-NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh, 201314, India
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8
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An C, Zhu F, Yao Y, Zhang K, Wang W, Zhang J, Wei G, Xia Y, Gao Q, Gao SS. Beyond the cyclopropyl ring formation: fungal Aj_EasH catalyzes asymmetric hydroxylation of ergot alkaloids. Appl Microbiol Biotechnol 2022; 106:2981-2991. [PMID: 35389067 DOI: 10.1007/s00253-022-11892-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/12/2022] [Accepted: 03/19/2022] [Indexed: 11/28/2022]
Abstract
Ergot alkaloids (EAs) are among the most important bioactive natural products. FeII/α-ketoglutarate-dependent dioxygenase Aj_EasH from Aspergillus japonicus is responsible for the formation of the cyclopropyl ring of the ergot alkaloid (EA) cycloclavine (4). Herein we reconstituted the biosynthesis of 4 in vitro from prechanoclavine (1) for the first time. Additionally, an unexpected activity of asymmetric hydroxylation at the C-4 position of EA compound festuclavine (5) for Aj_EasH was revealed. Furthermore, Aj_EasH also catalyzes the hydroxylation of two more EAs 9,10-dihydrolysergol (6) and elymoclavine (7). Thus, our results proved that Aj_EasH is a promiscuous and bimodal dioxygenase that catalyzes both the formation of cyclopropyl ring in 4 and the asymmetric hydroxylation of EAs. Molecular docking (MD) revealed the substrate-binding mode as well as the catalytic mechanism of asymmetric hydroxylation, suggesting more EAs could potentially be recognized and hydroxylated by Aj_EasH. Overall, the newly discovered activity empowered Aj_EasH with great potential for producing more diverse and bioactive EA derivatives. KEY POINTS: • Aj_EasH was revealed to be a promiscuous and bimodal FeII/α-ketoglutarate-dependent dioxygenase. • Aj_EasH converted festuclavine, 9,10-dihydrolysergol, and elymoclavine to their hydroxylated derivatives. • The catalytic mechanism of Aj_EasH for hydroxylation was analyzed by molecular docking.
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Affiliation(s)
- Chunyan An
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Biotechnology College of Tianjin University of Science and Technology, Tianjin, 300457, China. .,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Fangfang Zhu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Biotechnology College of Tianjin University of Science and Technology, Tianjin, 300457, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Kexin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yue Xia
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Qiang Gao
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Biotechnology College of Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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9
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Abstract
Polypharmacology is a concept where a molecule can interact with two or more targets simultaneously. It offers many advantages as compared to the conventional single-targeting molecules. A multi-targeting drug is much more efficacious due to its cumulative efficacy at all of its individual targets making it much more effective in complex and multifactorial diseases like cancer, where multiple proteins and pathways are involved in the onset and development of the disease. For a molecule to be polypharmacologic in nature, it needs to possess promiscuity which is the ability to interact with multiple targets; and at the same time avoid binding to antitargets which would otherwise result in off-target adverse effects. There are certain structural features and physicochemical properties which when present would help researchers to predict if the designed molecule would possess promiscuity or not. Promiscuity can also be identified via advanced state-of-the-art computational methods. In this review, we also elaborate on the methods by which one can intentionally incorporate promiscuity in their molecules and make them polypharmacologic. The polypharmacology paradigm of "one drug-multiple targets" has numerous applications especially in drug repurposing where an already established drug is redeveloped for a new indication. Though designing a polypharmacological drug is much more difficult than designing a single-targeting drug, with the current technologies and information regarding different diseases and chemical functional groups, it is plausible for researchers to intentionally design a polypharmacological drug and unlock its advantages.
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10
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Linciano S, Wong EL, Mazzocato Y, Chinellato M, Scaravetti T, Caregnato A, Cacco V, Romanyuk Z, Angelini A. Guidelines, Strategies, and Principles for the Directed Evolution of Cross-Reactive Antibodies Using Yeast Surface Display Technology. Methods Mol Biol 2022; 2491:251-262. [PMID: 35482195 DOI: 10.1007/978-1-0716-2285-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ability of cross-reactive antibodies to bind multiple related or unrelated targets derived from different species provides not only superior therapeutic efficacy but also a better assessment of treatment toxicity, thereby facilitating the transition from preclinical models to human clinical studies. This chapter provides some guidelines for the directed evolution of cross-reactive antibodies using yeast surface display technology. Cross-reactive antibodies are initially isolated from a naïve library by combining highly avid magnetic bead separations followed by multiple cycles of flow cytometry sorting. Once initial cross-reactive clones are identified, sequential rounds of mutagenesis and two-pressure selection strategies are applied to engineer cross-reactive antibodies with improved affinity and yet retained or superior cross-reactivity.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ee Lin Wong
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ylenia Mazzocato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Monica Chinellato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
- Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Tiziano Scaravetti
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alberto Caregnato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Veronica Cacco
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Zhanna Romanyuk
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy.
- European Centre for Living Technology (ECLT), Ca' Bottacin, Venice, Italy.
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11
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Abstract
Epitope-based vaccines is one of the most recent methodologies applied in bioinformatics studies. This strategy consists of identifying regions of the protein (peptides or epitopes) which show antigen properties capable of stimulating the immune system against proteins from virus, bacteria, fungi, etc. This chapter describes a general procedure to identify epitopes to be used as epitope vaccine using bioinformatics methods including primary protein sequence analyses, epitope predictor, docking, and molecular dynamics simulations for the selection of T- and B-cell epitopes.
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Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico
| | - G Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico
| | - Jazmin García-Machorro
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico.
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12
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Hu H, Bajorath J. Systematic assessment of structure- promiscuity relationships between different types of kinase inhibitors. Bioorg Med Chem 2021; 41:116226. [PMID: 34082305 DOI: 10.1016/j.bmc.2021.116226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/29/2022]
Abstract
Given the increasing quest for selective kinase inhibitors, we have systematically investigated structural and structure-promiscuity relationships between promiscuous kinase inhibitors and other types with increasing potential for selective kinase inhibition. Therefore, inhibitors with different modes of action were extracted from X-ray structures of kinase complexes. For more than 18,000 promiscuous kinase inhibitors and 1253 type I1/2, II, and allosteric inhibitors with structurally confirmed mechanisms, analogue space was systematically charted. These inhibitors were active against a total of 426 human kinases. While nearly 80% of the promiscuous inhibitors formed related analogues series, only ~30% of other types of inhibitors were involved in such structural relationships and many of these inhibitors also had multi-kinase activity. Thus, most of the investigated type I1/2, II, and allosteric inhibitors with reported single-kinase activity were distinguished from promiscuous inhibitors, thus indicating potential for kinase selectivity. Structural relationships between promiscuous inhibitors and the subset of other inhibitors were organized in a matrix format including kinase activity profiles, revealing structure-promiscuity relationships for follow-up investigations.
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13
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Li F, Xu Y, Wang C, Wang C, Zhao R, Wang L. Data for the lipase catalyzed synthesis of cyano-containing multi-substituted indoles. Data Brief 2021; 36:107045. [PMID: 33997196 DOI: 10.1016/j.dib.2021.107045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/20/2022] Open
Abstract
The data presented here are related to the research paper entitled “Efficient Synthesis of Cyano-containing Multi-substituted Indoles Catalyzed by Lipase” [1]. In this data article, the lipase catalyzed synthetic procedures for the preparation of multi-substituted indoles and their derivatives were described. In total, 11 compounds were obtained and the optimum pH, reaction time and substrate ratio were screened through this study.
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14
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Cea-Rama I, Coscolín C, Katsonis P, Bargiela R, Golyshin PN, Lichtarge O, Ferrer M, Sanz-Aparicio J. Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase. Comput Struct Biotechnol J 2021; 19:2307-2317. [PMID: 33995922 PMCID: PMC8105184 DOI: 10.1016/j.csbj.2021.04.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 01/02/2023] Open
Abstract
Our understanding of enzymes with high substrate ambiguity remains limited because their large active sites allow substrate docking freedom to an extent that seems incompatible with stereospecificity. One possibility is that some of these enzymes evolved a set of evolutionarily fitted sequence positions that stringently allow switching substrate ambiguity and chiral specificity. To explore this hypothesis, we targeted for mutation a serine ester hydrolase (EH3) that exhibits an impressive 71-substrate repertoire but is not stereospecific (e.e. 50%). We used structural actions and the computational evolutionary trace method to explore specificity-swapping sequence positions and hypothesized that position I244 was critical. Driven by evolutionary action analysis, this position was substituted to leucine, which together with isoleucine appears to be the amino acid most commonly present in the closest homologous sequences (max. identity, ca. 67.1%), and to phenylalanine, which appears in distant homologues. While the I244L mutation did not have any functional consequences, the I244F mutation allowed the esterase to maintain a remarkable 53-substrate range while gaining stereospecificity properties (e.e. 99.99%). These data support the possibility that some enzymes evolve sequence positions that control the substrate scope and stereospecificity. Such residues, which can be evolutionarily screened, may serve as starting points for further designing substrate-ambiguous, yet chiral-specific, enzymes that are greatly appreciated in biotechnology and synthetic chemistry.
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Affiliation(s)
- Isabel Cea-Rama
- Institute of Physical Chemistry “Rocasolano”, CSIC, 28006 Madrid, Spain
| | | | | | - Rafael Bargiela
- Centre for Environmental Biotechnology, Bangor University, LL57 2UW Bangor, UK
| | - Peter N. Golyshin
- Centre for Environmental Biotechnology, Bangor University, LL57 2UW Bangor, UK
- School of Natural Sciences, Bangor University, LL57 2UW Bangor, UK
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15
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Li F, Xu Y, Wang C, Wang C, Zhao R, Wang L. Efficient synthesis of cyano-containing multi-substituted indoles catalyzed by lipase. Bioorg Chem 2021; 107:104583. [PMID: 33421956 DOI: 10.1016/j.bioorg.2020.104583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Indoles are important bioactive compounds that have been extensively studied in organic chemistry. In this work, a green and efficient process for the synthesis of Indoles from 1,3-diketones with fumaronitrile was developed. RESULTS Under optimal conditions (1,3-diketones (0.5 mmol), fumaronitrile (1 mmol), water (2 ml), lipase (15 mg), 30 °C, 24 h), high yields and satisfactory regioselectivity of cyano-containing multi-substituted indoles could be obtained when CRL (C. rugosa lipase) was used as the catalyst. CONCLUSION This enzymatic method demonstrates the great potential for the synthesis of indoles and extends the application of enzyme in organic synthesis.
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16
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Ochoa R, Magnitov M, Laskowski RA, Cossio P, Thornton JM. An automated protocol for modelling peptide substrates to proteases. BMC Bioinformatics 2020; 21:586. [PMID: 33375946 PMCID: PMC7771086 DOI: 10.1186/s12859-020-03931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/09/2020] [Indexed: 11/21/2022] Open
Abstract
Background Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition.
Results As an application, we modelled a subset of protease–peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease–specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease’s substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches. Conclusion Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease–peptide complexes.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, 050010, Medellín, Colombia. .,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Mikhail Magnitov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia, 141701
| | - Roman A Laskowski
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, 050010, Medellín, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Noda-Garcia L, Tawfik DS. Enzyme evolution in natural products biosynthesis: target- or diversity-oriented? Curr Opin Chem Biol 2020; 59:147-154. [PMID: 32771972 DOI: 10.1016/j.cbpa.2020.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022]
Abstract
Natural product biosynthesis (NPB) is the Panda's Thumb of evolutionary biochemistry. Arm races between organisms, and ever-changing environments, result in relentless innovation. This review focusses on enzyme evolution in NPB. First, we review cases of de novo emergence, whereby a completely new enzymatic activity arose in a ligand-binding protein, or a new enzyme emerged including a completely new scaffold. Second, we briefly review the current models for enzyme evolution, and how they explain the inherent promiscuity of NPB enzymes and their tendency to produce multiple related products. We thus suggest that NPB enzymes a priori evolved to generate a specific product; they are, however, trapped in a multifunctional, generalist evolutionary state and thereby produce a diversity of products.
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Affiliation(s)
- Lianet Noda-Garcia
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel.
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18
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Daletos G, Stephanopoulos G. Protein engineering strategies for microbial production of isoprenoids. Metab Eng Commun 2020; 11:e00129. [PMID: 32612930 DOI: 10.1016/j.mec.2020.e00129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/06/2020] [Accepted: 04/24/2020] [Indexed: 01/16/2023] Open
Abstract
Isoprenoids comprise one of the most chemically diverse family of natural products with high commercial interest. The structural diversity of isoprenoids is mainly due to the modular activity of three distinct classes of enzymes, including prenyl diphosphate synthases, terpene synthases, and cytochrome P450s. The heterologous expression of these enzymes in microbial systems is suggested to be a promising sustainable way for the production of isoprenoids. Several limitations are associated with native enzymes, such as low stability, activity, and expression profiles. To address these challenges, protein engineering has been applied to improve the catalytic activity, selectivity, and substrate turnover of enzymes. In addition, the natural promiscuity and modular fashion of isoprenoid enzymes render them excellent targets for combinatorial studies and the production of new-to-nature metabolites. In this review, we discuss key individual and multienzyme level strategies for the successful implementation of enzyme engineering towards efficient microbial production of high-value isoprenoids. Challenges and future directions of protein engineering as a complementary strategy to metabolic engineering are likewise outlined. Isoprenoid enzymes are attractive biocatalysts for protein engineering. Isoprenoid enzymes can be engineered for broader substrate promiscuity. Protein engineering can lead to the production of non-natural isoprenoids. Protein engineering can promote co-localization of isoprenoid pathway enzymes. Protein engineering supplements combinatorial biosynthesis for isoprenoid synthesis.
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19
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Shamseldin A, Velázquez E. The promiscuity of Phaseolus vulgaris L. (common bean) for nodulation with rhizobia: a review. World J Microbiol Biotechnol 2020; 36:63. [PMID: 32314065 DOI: 10.1007/s11274-020-02839-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/09/2020] [Indexed: 11/24/2022]
Abstract
Phaseolus vulgaris L. (common bean) is a legume indigenous to American countries currently cultivated in all continents, which is nodulated by different rhizobial species and symbiovars. Most of species able to nodulate this legume worldwide belong to the genus Rhizobium, followed by those belonging to the genera Ensifer (formerly Sinorhizobium) and Pararhizobium (formerly Rhizobium) and minority by species of the genus Bradyrhizobium. All these genera belong to the phylum alpha-Proteobacteria, but the nodulation of P. vulgaris has also been reported for some species belonging to Paraburkholderia and Cupriavidus from the beta-Proteobacteria. Several species nodulating P. vulgaris were originally isolated from nodules of this legume in American countries and are linked to the symbiovars phaseoli and tropici, which are currently present in other continents probably because they were spread in their soils together with the P. vulgaris seeds. In addition, this legume can be nodulated by species and symbiovars originally isolated from nodules of other legumes due its high promiscuity, a concept currently related with the ability of a legume to be nodulated by several symbiovars rather than by several species. In this article we review the species and symbiovars able to nodulate P. vulgaris in different countries and continents and the challenges on the study of the P. vulgaris endosymbionts diversity in those countries where they have not been studied yet, that will allow to select highly effective rhizobial strains in order to guarantee the success of P. vulgaris inoculation.
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Affiliation(s)
- Abdelaal Shamseldin
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, New Borg El-Arab, Alexandria, Egypt.
| | - Encarna Velázquez
- Departamento de Microbiología Y Genética and CIALE, Universidad de Salamanca, Salamanca, Spain.,Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain
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20
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Durand S, Braquart-Varnier C, Beltran-Bech S. Promiscuity and sex ratio in the terrestrial isopod Armadillidium vulgare and consequences on genetic diversity. Behav Processes 2020; 171:104030. [PMID: 31899276 DOI: 10.1016/j.beproc.2019.104030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/03/2019] [Accepted: 12/27/2019] [Indexed: 11/21/2022]
Abstract
In promiscuous mating systems, both males and females mate with several partners. While the benefits of multiple mating are well recognized for males, there are several non-mutually exclusive hypotheses to explain multiple mating for females. Promiscuity is widespread in terrestrial isopods. Here, we placed experimental populations of the terrestrial isopod Armadillidium vulgare under varying sex ratios to manipulate the number of available partners, and better characterise the mating system in this species by performing paternity tests using microsatellite markers. We observed that females usually mate multiply with up to 5 males in a single event of reproduction. A higher number of fathers in broods did not increase brood size nor heterozygosity, but increased allelic richness. Promiscuity seems to be asymmetric in this species, with females being less affected by changes in sex ratio than were males and would be an adaptive mating system maximising the offspring genetic diversity.
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21
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Wang K, Cao R, Wang M, Lin Q, Zhan R, Xu H, Wang S. A novel thermostable GH10 xylanase with activities on a wide variety of cellulosic substrates from a xylanolytic Bacillus strain exhibiting significant synergy with commercial Celluclast 1.5 L in pretreated corn stover hydrolysis. Biotechnol Biofuels 2019; 12:48. [PMID: 30899328 PMCID: PMC6408826 DOI: 10.1186/s13068-019-1389-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/25/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Cellulose and hemicellulose are the two largest components in lignocellulosic biomass. Enzymes with activities towards cellulose and xylan have attracted great interest in the bioconversion of lignocellulosic biomass, since they have potential in improving the hydrolytic performance and reducing the enzyme costs. Exploring glycoside hydrolases (GHs) with good thermostability and activities on xylan and cellulose would be beneficial to the industrial production of biofuels and bio-based chemicals. RESULTS A novel GH10 enzyme (XynA) identified from a xylanolytic strain Bacillus sp. KW1 was cloned and expressed. Its optimal pH and temperature were determined to be pH 6.0 and 65 °C. Stability analyses revealed that XynA was stable over a broad pH range (pH 6.0-11.0) after being incubated at 25 °C for 24 h. Moreover, XynA retained over 95% activity after heat treatment at 60 °C for 60 h, and its half-lives at 65 °C and 70 °C were about 12 h and 1.5 h, respectively. More importantly, in terms of substrate specificity, XynA exhibits hydrolytic activities towards xylans, microcrystalline cellulose (filter paper and Avicel), carboxymethyl cellulose (CMC), cellobiose, p-nitrophenyl-β-d-cellobioside (pNPC), and p-nitrophenyl-β-d-glucopyranoside (pNPG). Furthermore, the addition of XynA into commercial cellulase in the hydrolysis of pretreated corn stover resulted in remarkable increases (the relative increases may up to 90%) in the release of reducing sugars. Finally, it is worth mentioning that XynA only shows high amino acid sequence identity (88%) with rXynAHJ14, a GH10 xylanase with no activity on CMC. The similarities with other characterized GH10 enzymes, including xylanases and bifunctional xylanase/cellulase enzymes, are no more than 30%. CONCLUSIONS XynA is a novel thermostable GH10 xylanase with a wide substrate spectrum. It displays good stability in a broad range of pH and high temperatures, and exhibits activities towards xylans and a wide variety of cellulosic substrates, which are not found in other GH10 enzymes. The enzyme also has high capacity in saccharification of pretreated corn stover. These characteristics make XynA a good candidate not only for assisting cellulase in lignocellulosic biomass hydrolysis, but also for the research on structure-function relationship of bifunctional xylanase/cellulase.
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Affiliation(s)
- Kui Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Ruoting Cao
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Meiling Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Qibin Lin
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Hui Xu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
- Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
| | - Sidi Wang
- College of Fundamental Medical Science, Guangzhou University of Chinese Medicine, Guangzhou Higher Education Mega Center, No.232 Outer Ring West Rd., Panyu District, Guangzhou, 510006 Guangdong China
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Morales JF, Alberca LN, Chuguransky S, Di Ianni ME, Talevi A, Ruiz ME. Molecular Topology and Other Promiscuity Determinants as Predictors of Therapeutic Class - A Theoretical Framework to Guide Drug Repositioning? Curr Top Med Chem 2018; 18:1110-1122. [PMID: 30068278 DOI: 10.2174/1568026618666180801091642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/08/2018] [Accepted: 07/25/2018] [Indexed: 11/22/2022]
Abstract
Much interest has been paid in the last decade on molecular predictors of promiscuity, including molecular weight, log P, molecular complexity, acidity constant and molecular topology, with correlations between promiscuity and those descriptors seemingly being context-dependent. It has been observed that certain therapeutic categories (e.g. mood disorders therapies) display a tendency to include multi-target agents (i.e. selective non-selectivity). Numerous QSAR models based on topological descriptors suggest that the topology of a given drug could be used to infer its therapeutic applications. Here, we have used descriptive statistics to explore the distribution of molecular topology descriptors and other promiscuity predictors across different therapeutic categories. Working with the publicly available ChEMBL database and 14 molecular descriptors, both hierarchical and non-hierchical clustering methods were applied to the descriptors mean values of the therapeutic categories after the refinement of the database (770 drugs grouped into 34 therapeutic categories). On the other hand, another publicly available database (repoDB) was used to retrieve cases of clinically-approved drug repositioning examples that could be classified into the therapeutic categories considered by the aforementioned clusters (111 cases), and the correspondence between the two studies was evaluated. Interestingly, a 3- cluster hierarchical clustering scheme based on only 14 molecular descriptors linked to promiscuity seem to explain up to 82.9% of approved cases of drug repurposing retrieved of repoDB. Therapeutic categories seem to display distinctive molecular patterns, which could be used as a basis for drug screening and drug design campaigns, and to unveil drug repurposing opportunities between particular therapeutic categories.
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Affiliation(s)
- Juan F Morales
- Departamento de Ciencias Biologicas, Laboratorio de Investigacion y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (B1900AJI) La Plata, Buenos Aires, Argentina.,Argentinean National Council for Scientific and Technical Research (CONICET) - CCT La Plata (B1900AJI), Buenos Aires, Argentina
| | - Lucas N Alberca
- Departamento de Ciencias Biologicas, Laboratorio de Investigacion y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (B1900AJI) La Plata, Buenos Aires, Argentina.,Argentinean National Council for Scientific and Technical Research (CONICET) - CCT La Plata (B1900AJI), Buenos Aires, Argentina
| | - Sara Chuguransky
- Departamento de Ciencias Biologicas, Laboratorio de Investigacion y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (B1900AJI) La Plata, Buenos Aires, Argentina.,Argentinean National Council for Scientific and Technical Research (CONICET) - CCT La Plata (B1900AJI), Buenos Aires, Argentina
| | - Mauricio E Di Ianni
- Departamento de Ciencias Biologicas, Laboratorio de Investigacion y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (B1900AJI) La Plata, Buenos Aires, Argentina.,Argentinean National Council for Scientific and Technical Research (CONICET) - CCT La Plata (B1900AJI), Buenos Aires, Argentina
| | - Alan Talevi
- Departamento de Ciencias Biologicas, Laboratorio de Investigacion y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (B1900AJI) La Plata, Buenos Aires, Argentina.,Argentinean National Council for Scientific and Technical Research (CONICET) - CCT La Plata (B1900AJI), Buenos Aires, Argentina.,Biopharmacy, Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata (UNLP), La Plata (B1900AJI), Buenos Aires, Argentina
| | - Maria E Ruiz
- Departamento de Ciencias Biologicas, Laboratorio de Investigacion y Desarrollo de Bioactivos (LIDeB), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (B1900AJI) La Plata, Buenos Aires, Argentina.,Argentinean National Council for Scientific and Technical Research (CONICET) - CCT La Plata (B1900AJI), Buenos Aires, Argentina.,Department of Biological Sciences, Quality Control of Drugs, Faculty of Exact Sciences, National University of La Plata (UNLP), La Plata (B1900AJI), Buenos Aires, Argentina
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23
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Banerjee A, Hamberger B. P450s controlling metabolic bifurcations in plant terpene specialized metabolism. Phytochem Rev 2018; 17:81-111. [PMID: 29563859 PMCID: PMC5842272 DOI: 10.1007/s11101-017-9530-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/20/2017] [Indexed: 05/18/2023]
Abstract
ABSTRACT Catalyzing stereo- and regio-specific oxidation of inert hydrocarbon backbones, and a range of more exotic reactions inherently difficult in formal chemical synthesis, cytochromes P450 (P450s) offer outstanding potential for biotechnological engineering. Plants and their dazzling diversity of specialized metabolites have emerged as rich repository for functional P450s with the advances of deep transcriptomics and genome wide discovery. P450s are of outstanding interest for understanding chemical diversification throughout evolution, for gaining mechanistic insights through the study of their structure-function relationship, and for exploitation in Synthetic Biology. In this review, we highlight recent developments and examples in the discovery of plant P450s involved in the biosynthesis of industrially relevant monoterpenoids, sesquiterpenoids, diterpenoids and triterpenoids, throughout 2016 and early 2017. Examples were selected to illustrate the spectrum of value from commodity chemicals, flavor and fragrance compounds to pharmacologically active terpenoids. We focus on a recently emerging theme, where P450s control metabolic bifurcations and chemical diversity of the final product profile, either within a pathway, or through neo-functionalization in related species. The implications may inform approaches for rational assembly of recombinant pathways, biotechnological production of high value terpenoids and generation of novel chemical entities.
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Affiliation(s)
- Aparajita Banerjee
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824 USA
| | - Björn Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824 USA
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24
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Yardeni EH, Zomot E, Bibi E. The fascinating but mysterious mechanistic aspects of multidrug transport by MdfA from Escherichia coli. Res Microbiol 2017; 169:455-460. [PMID: 28951231 DOI: 10.1016/j.resmic.2017.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/24/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
Abstract
MdfA is an interesting member of a large group of secondary multidrug (Mdr) transporters. Through genetic, biochemical and biophysical studies of MdfA, many challenging aspects of the multidrug transport phenomenon have been addressed. This includes its ability to interact with chemically unrelated drugs and how it utilizes energy to drive efflux of compounds that are not only structurally, but also electrically, different. Admittedly, however, despite all efforts and a recent pioneering structural contribution, several important mechanistic issues of the promiscuous capabilities of MdfA still seek better molecular and dynamic understanding.
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Affiliation(s)
- Eliane H Yardeni
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elia Zomot
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eitan Bibi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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25
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Chartier M, Morency LP, Zylber MI, Najmanovich RJ. Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. BMC Pharmacol Toxicol 2017; 18:18. [PMID: 28449705 PMCID: PMC5408384 DOI: 10.1186/s40360-017-0128-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/28/2017] [Indexed: 01/21/2023] Open
Abstract
Background Promiscuity in molecular interactions between small-molecules, including drugs, and proteins is widespread. Such unintended interactions can be exploited to suggest drug repurposing possibilities as well as to identify potential molecular mechanisms responsible for observed side-effects. Methods We perform a large-scale analysis to detect binding-site molecular interaction field similarities between the binding-sites of the primary target of 400 drugs against a dataset of 14082 cavities within 7895 different proteins representing a non-redundant dataset of all proteins with known structure. Statistically-significant cases with high levels of similarities represent potential cases where the drugs that bind the original target may in principle bind the suggested off-target. Such cases are further analysed with docking simulations to verify if indeed the drug could, in principle, bind the off-target. Diverse sources of data are integrated to associated potential cross-reactivity targets with side-effects. Results We observe that promiscuous binding-sites tend to display higher levels of hydrophobic and aromatic similarities. Focusing on the most statistically significant similarities (Z-score ≥ 3.0) and corroborating docking results (RMSD < 2.0 Å), we find 2923 cases involving 140 unique drugs and 1216 unique potential cross-reactivity protein targets. We highlight a few cases with a potential for drug repurposing (acetazolamide as a chorismate pyruvate lyase inhibitor, raloxifene as a bacterial quorum sensing inhibitor) as well as to explain the side-effects of zanamivir and captopril. A web-interface permits to explore the detected similarities for each of the 400 binding-sites of the primary drug targets and visualise them for the most statistically significant cases. Conclusions The detection of molecular interaction field similarities provide the opportunity to suggest drug repurposing opportunities as well as to identify potential molecular mechanisms responsible for side-effects. All methods utilized are freely available and can be readily applied to new query binding-sites. All data is freely available and represents an invaluable source to identify further candidates for repurposing and suggest potential mechanisms responsible for side-effects. Electronic supplementary material The online version of this article (doi:10.1186/s40360-017-0128-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthieu Chartier
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada
| | - Louis-Philippe Morency
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada
| | - María Inés Zylber
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada.,Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Québec, Canada
| | - Rafael J Najmanovich
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Québec, Canada. .,Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Québec, Canada.
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26
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Bahia MS, Nissim I, Niv MY. Bitterness prediction in-silico: A step towards better drugs. Int J Pharm 2017; 536:526-529. [PMID: 28363856 DOI: 10.1016/j.ijpharm.2017.03.076] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 11/30/2022]
Abstract
Bitter taste is innately aversive and thought to protect against consuming poisons. Bitter taste receptors (Tas2Rs) are G-protein coupled receptors, expressed both orally and extra-orally and proposed as novel targets for several indications, including asthma. Many clinical drugs elicit bitter taste, suggesting the possibility of drugs re-purposing. On the other hand, the bitter taste of medicine presents a major compliance problem for pediatric drugs. Thus, efficient tools for predicting, measuring and masking bitterness of active pharmaceutical ingredients (APIs) are required by the pharmaceutical industry. Here we highlight the BitterDB database of bitter compounds and survey the main computational approaches to prediction of bitter taste based on compound's chemical structure. Current in silico bitterness prediction methods provide encouraging results, can be constantly improved using growing experimental data, and present a reliable and efficient addition to the APIs development toolbox.
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Affiliation(s)
- Malkeet Singh Bahia
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, 91904, Israel
| | - Ido Nissim
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, 91904, Israel
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, 91904, Israel.
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27
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Jaiswal SK, Msimbira LA, Dakora FD. Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut (Arachis hypogaea L.) in South Africa. Syst Appl Microbiol 2017; 40:215-226. [PMID: 28372899 PMCID: PMC5460907 DOI: 10.1016/j.syapm.2017.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/05/2017] [Accepted: 02/12/2017] [Indexed: 11/30/2022]
Abstract
Groundnut is an economically important N2-fixing legume that can contribute about 100–190 kg N ha−1 to cropping systems. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was done using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1415 bp. The rhizobial isolates were grouped into five main clusters with Jaccard's similarity coefficient of 0.00–1.00, and 35 restriction types in a UPGMA dendrogram. Partial sequence analysis of the 16S rDNA, IGS of 16S rDNA-23S rDNA, atpD, gyrB, gltA, glnII and symbiotic nifH and nodC genes obtained for representative isolates of each RFLP-cluster showed that these native groundnut-nodulating rhizobia were phylogenetically diverse, thus confirming the extent of promiscuity of this legume. Concatenated gene sequence analysis showed that most isolates did not align with known type strains, and may represent new species from South Africa. This underscored the high genetic variability associated with groundnut Rhizobium and Bradyrhizobium in South African soils, and the possible presence of a reservoir of novel groundnut-nodulating Bradyrhizobium and Rhizobium in the country.
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Affiliation(s)
- Sanjay K Jaiswal
- Department of Chemistry, Tshwane University of Technology, Pretoria, South Africa.
| | - Levini A Msimbira
- Department of Crop Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - Felix D Dakora
- Department of Chemistry, Tshwane University of Technology, Pretoria, South Africa.
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28
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Lee ECY, Steeno G, Wassermann AM, Zhang L, Shah F, Price DA. Amine promiscuity and toxicology analysis. Bioorg Med Chem Lett 2016; 27:653-657. [PMID: 28011216 DOI: 10.1016/j.bmcl.2016.11.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 12/22/2022]
Abstract
Drug discovery programs often face challenges to obtain sufficient duration of action of the drug (i.e. seek longer half-lives). If the pharmacodynamic response is driven by free plasma concentration of the drug then extending the plasma drug concentration is a valid approach. Half-life is dependent on the volume of distribution, which in turn can be dependent upon the ionization state of the molecule. Basic compounds tend to have a higher volume of distribution leading to longer half-lives. However, it has been shown that bases may also have higher promiscuity. In this work, we describe an analysis of in vitro pharmacological profiling and toxicology data investigating the role of primary, secondary, and tertiary amines in imparting promiscuity and thus off-target toxicity. Primary amines are found to be less promiscuous in in vitro assays and have improved profiles in in vivo toxicology studies compared to secondary and tertiary amines.
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Affiliation(s)
- Esther C Y Lee
- Medicine Design, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States.
| | - Gregory Steeno
- Research Statistics, Pfizer Worldwide Research & Development, Groton, CT 06340, United States
| | | | - Liying Zhang
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
| | - Falgun Shah
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
| | - David A Price
- Medicine Design, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
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29
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Zhou J, Huang X, Zhang Z, Song P, Li Y. Trypsin-catalyzed multicomponent reaction: A novel and efficient one-pot synthesis of thiazole-2-imine derivatives. J Biotechnol 2016; 241:14-21. [PMID: 27825826 DOI: 10.1016/j.jbiotec.2016.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/25/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022]
Abstract
The first Trypsin from porcine pancreas catalyzed a novel one-pot three-component reaction of α-bromoketone, primary alkylamines, and phenylisothiocyanate for the synthesis of thiazole-imine derivatives with high yields (up to 98%) in a short time under mild conditions. The results revealed that Trypsin exhibited excellent catalytic activity and great tolerance for broad substrates. This Trypsin-catalyzed three component convergent method provides a novel strategy for the synthesis of thiazole-2-imine derivatives and expands the promiscuous functions of enzymes in organic synthesis.
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Affiliation(s)
- Junbin Zhou
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Xingtian Huang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Zhuan Zhang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Ping Song
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Yiqun Li
- Department of Chemistry, Jinan University, Guangzhou 510632, China.
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30
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Droge-Young EM, Belote JM, Perez GS, Pitnick S. Resolving mechanisms of short-term competitive fertilization success in the red flour beetle. J Insect Physiol 2016; 93-94:1-10. [PMID: 27343847 DOI: 10.1016/j.jinsphys.2016.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Postcopulatory sexual selection occurs when sperm from multiple males occupy a female's reproductive tract at the same time and is expected to generate strong selection pressures on traits related to competitive fertilization success. However, knowledge of competitive fertilization success mechanisms and characters targeted by resulting selection is limited, partially due to the difficulty of discriminating among sperm from different males within the female reproductive tract. Here, we resolved mechanisms of competitive fertilization success in the promiscuous flour beetle Tribolium castaneum. Through creation of transgenic lines with fluorescent-tagged sperm heads, we followed the fate of focal male sperm in female reproductive tracts while tracking paternity across numerous rematings. Our results indicate that a given male's sperm persist and fertilize eggs through at least seven rematings. Additionally, the proportion of a male's sperm in the bursa (the site of spermatophore deposition), which is influenced by both timing of female's ejecting excess sperm and male size, significantly predicted paternity share in the 24h following a mating. Contrary to expectation, proportional representation of sperm within the female's specialized sperm-storage organ did not significantly predict paternity, though spermathecal sperm may play a role in fertilization when females do not have access to mates for longer time periods. We address the adaptive significance of the identified reproductive mechanisms in the context of T. castaneum's unique mating system and ecology.
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Affiliation(s)
| | - John M Belote
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Giselle S Perez
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Scott Pitnick
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
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31
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Mariutti RB, Ullah A, Araujo GC, Murakami MT, Arni RK. Tyrosine binding and promiscuity in the arginine repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis. Biochem Biophys Res Commun 2016; 475:350-5. [PMID: 27233609 DOI: 10.1016/j.bbrc.2016.05.091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/19/2016] [Indexed: 11/17/2022]
Abstract
The arginine repressor (ArgR) regulates arginine biosynthesis in a number of microorganisms and consists of two domains interlinked by a short peptide; the N-terminal domain is involved in DNA binding and the C-terminal domain binds arginine and forms a hexamer made-up of a dimer of trimers. The crystal structure of the C-terminal domain of ArgR from the pathogenic Corynebacterium pseudotuberculosis determined at 1.9 Å resolution contains a tightly bound tyrosine at the arginine-binding site indicating hitherto unobserved promiscuity. Structural analysis of the binding pocket displays clear molecular adaptations to accommodate tyrosine binding suggesting the possible existence of an alternative regulatory process in this pathogenic bacterium.
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Affiliation(s)
- Ricardo Barros Mariutti
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil.
| | - Anwar Ullah
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil; Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Islamabad 45550, Pakistan
| | | | - Mario Tyago Murakami
- Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil
| | - Raghuvir Krishnaswamy Arni
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil; Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil.
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32
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Abstract
BACKGROUND Small molecules are information carriers that make cells aware of external changes and couple internal metabolic and signalling pathway systems with each other. In some specific physiological status, natural or artificial molecules are used to interact with selective biological targets to activate or inhibit their functions to achieve expected biological and physiological output. Millions of years of evolution have optimized biological processes and pathways and now the endocrine and immune system cannot work properly without some key small molecules. In the past thousands of years, the human race has managed to find many medicines against diseases by trail-and-error experience. In the recent decades, with the deepening understanding of life and the progress of molecular biology, researchers spare no effort to design molecules targeting one or two key enzymes and receptors related to corresponding diseases. But recent studies in pharmacogenomics have shown that polypharmacology may be necessary for the effects of drugs, which challenge the paradigm, 'one drug, one target, one disease'. Nowadays, cheminformatics and structural biology can help us reasonably take advantage of the polypharmacology to design next-generation promiscuous drugs and drug combination therapies. RESULTS 234,591 protein-ligand interactions were extracted from ChEMBL. By the 2D structure similarity, 13,769 ligand emerged from 156,151 distinct ligands which were recognized by 1477 proteins. Ligand cluster- and sequence-based protein networks (LCBN, SBN) were constructed, compared and analysed. For assisting compound designing, exploring polypharmacology and finding possible drug combination, we integrated the pathway, disease, drug adverse reaction and the relationship of targets and ligand clusters into the web platform, ePlatton, which is available at http://www.megabionet.org/eplatton. CONCLUSIONS Although there were some disagreements between the LCBN and SBN, communities in both networks were largely the same with normalized mutual information at 0.9. The study of target and ligand cluster promiscuity underlying the LCBN showed that light ligand clusters were more promiscuous than the heavy one and that highly connected nodes tended to be protein kinases and involved in phosphorylation. ePlatton considerably reduced the redundancy of the ligand set of targets and made it easy to deduce the possible relationship between compounds and targets, pathways and side effects. ePlatton behaved reliably in validation experiments and also fast in virtual screening and information retrieval.Graphical abstractCluster exemplars and ePlatton's mechanism.
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Affiliation(s)
- Yu Du
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
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33
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MacFarlane GR, Vasey PL. Promiscuous primates engage in same-sex genital interactions. Behav Processes 2016; 126:21-6. [PMID: 26930251 DOI: 10.1016/j.beproc.2016.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/26/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
Same-sex genital interactions (SSGIs) occur across the order primates, yet explaining their maintenance in evolutionary terms appears problematic; as such interactions seem to counteract reproductive goals. We hypothesised that in more promiscuous species, where sexual motivation, mating effort, and non-conceptive heterosexual behaviour are greater, SSGIs may also occur at greater frequencies without necessarily impeding reproduction. We found that the expression of both male and female SSGIs were greater in multimale systems than in unimale ones. Both male and female SSGIs were positively correlated with the degree of promiscuity (relative testes mass). As mating system confers biases in the sex ratio that may influence the expression of SSGIs, we controlled for availability of members of the same-sex. When employing this control, results were largely congruent. For males, SSGIs were expressed more frequently in multimale systems. For both sexes, SSGIs were expressed more frequently with greater relative testes mass. We suggest SSGIs in primates may be a neutral by-product of selection for increases in promiscuous sexual activity, and that in certain instances these interactions may be co-opted to facilitate adaptive social functions.
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Affiliation(s)
- Geoff R MacFarlane
- School of Environmental and Life Sciences, University of Newcastle, Australia.
| | - Paul L Vasey
- Department of Psychology, University of Lethbridge, Canada
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34
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Abstract
This Special Issue on the topic of Steroid and Sterol Signaling: Promiscuity and Diversity, dwells on the growing realization that the 'one ligand, one binding site' and 'one enzyme, one reaction' concepts are out of date. Focusing on cytochromes P450 (CYP), hydroxysteroid dehydrogenases (HSDs), and related enzymes, the Special Issue highlights that a single enzyme can bind to diverse substrates, and in different conformations, and can catalyze multiple different conversions (and in different directions), thereby, generating an unexpectedly wide spectrum of ligands that can have subtly different biological actions. This article is part of a Special Issue entitled 'Steroid/Sterol Signaling' .
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Affiliation(s)
- Richard Lathe
- Pieta Research, Edinburgh, UK; Pushchino State University and Institute of Bioorganic Chemistry, Moscow Region, Russian Federation.
| | - Yuri Kotelevtsev
- Skolkovo Institute of Science and Technology, Moscow Region, Russian Federation
| | - J Ian Mason
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK.
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35
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Chang TC, Stergiopoulos I. Evolutionary analysis of the global landscape of protein domain types and domain architectures associated with family 14 carbohydrate-binding modules. FEBS Lett 2015; 589:1813-8. [PMID: 26067847 DOI: 10.1016/j.febslet.2015.05.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/11/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
Abstract
Domain promiscuity is a powerful evolutionary force that promotes functional innovation in proteins, thus increasing proteome and organismal complexity. Carbohydrate-binding modules, in particular, are known to partake in complex modular architectures that play crucial roles in numerous biochemical and molecular processes. However, the extent, functional, and evolutionary significance of promiscuity is shrouded in mystery for most CBM families. Here, we analyzed the global promiscuity of family 14 carbohydrate-binding modules (CBM14s) and show that fusion, fission, and reorganization events with numerous other domain types interplayed incessantly in a lineage-dependent manner to likely facilitate species adaptation and functional innovation in the family.
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Affiliation(s)
- Ti-Cheng Chang
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
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Beaulieu PL, Bolger G, Deon D, Duplessis M, Fazal G, Gagnon A, Garneau M, LaPlante S, Stammers T, Kukolj G, Duan J. Multi-parameter optimization of aza-follow-ups to BI 207524, a thumb pocket 1 HCV NS5B polymerase inhibitor. Part 2: Impact of lipophilicity on promiscuity and in vivo toxicity. Bioorg Med Chem Lett 2015; 25:1140-5. [PMID: 25599836 DOI: 10.1016/j.bmcl.2014.12.078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 12/20/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
Abstract
We describe our efforts to identify analogs of thumb pocket 1 HCV NS5B inhibitor 1 (aza-analog of BI 207524) with improved plasma to liver partitioning and a predicted human half-life consistent with achieving a strong antiviral effect at a reasonable dose in HCV-infected patients. Compounds 3 and 7 were identified that met these criteria but exhibited off-target promiscuity in an in vitro pharmacology screen and in vivo toxicity in rats. High lipophilicity in this class was found to correlate with increased probability for promiscuous behavior and toxicity. The synthesis of an 8×11 matrix of analogs allowed the identification of C3, an inhibitor that displayed comparable potency to 1, improved partitioning to the liver and reduced lipophilicity. Although C3 displayed reduced propensity for in vitro off-target inhibition and the toxicity profile in rats was improved, the predicted human half-life of this compound was short, resulting in unacceptable dosing requirements to maintain a strong antiviral effect in patients.
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Affiliation(s)
- Pierre L Beaulieu
- Medicinal Chemistry Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Gordon Bolger
- Biology Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Dan Deon
- Medicinal Chemistry Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Martin Duplessis
- Medicinal Chemistry Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Gulrez Fazal
- Medicinal Chemistry Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Alexandre Gagnon
- Medicinal Chemistry Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Michel Garneau
- Biology Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Steven LaPlante
- Medicinal Chemistry Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Timothy Stammers
- Medicinal Chemistry Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - George Kukolj
- Biology Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
| | - Jianmin Duan
- Biology Department, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada
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Wang R, Chen R, Li J, Liu X, Xie K, Chen D, Yin Y, Tao X, Xie D, Zou J, Yang L, Dai J. Molecular characterization and phylogenetic analysis of two novel regio-specific flavonoid prenyltransferases from Morus alba and Cudrania tricuspidata. J Biol Chem 2014; 289:35815-25. [PMID: 25361766 DOI: 10.1074/jbc.m114.608265] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prenylated flavonoids are attractive specialized metabolites with a wide range of biological activities and are distributed in several plant families. The prenylation catalyzed by prenyltransferases represents a Friedel-Crafts alkylation of the flavonoid skeleton in the biosynthesis of natural prenylated flavonoids and contributes to the structural diversity and biological activities of these compounds. To date, all identified plant flavonoid prenyltransferases (FPTs) have been identified in Leguminosae. In the present study two new FPTs, Morus alba isoliquiritigenin 3'-dimethylallyltransferase (MaIDT) and Cudrania tricuspidata isoliquiritigenin 3'-dimethylallyltransferase (CtIDT), were identified from moraceous plants M. alba and C. tricuspidata, respectively. MaIDT and CtIDT shared low levels of homology with the leguminous FPTs. MaIDT and CtIDT are predicted to be membrane-bound proteins with predicted transit peptides, seven transmembrane regions, and conserved functional domains that are similar to other homogentisate prenyltransferases. Recombinant MaIDT and CtIDT were able to regioselectively introduce dimethylallyl diphosphate into the A ring of three flavonoids with different skeleton types (chalcones, isoflavones, and flavones). Phylogenetic analysis revealed that MaIDT and CtIDT are distantly related to their homologs in Leguminosae, which suggests that FPTs in Moraceae and Leguminosae might have evolved independently. MaIDT and CtIDT represent the first two non-Leguminosae FPTs to be identified in plants and could thus lead to the identification of additional evolutionarily varied FPTs in other non-Leguminosae plants and could elucidate the biosyntheses of prenylated flavonoids in various plants. Furthermore, MaIDT and CtIDT might be used for regiospecific prenylation of flavonoids to produce bioactive compounds for potential therapeutic applications due to their high efficiency and catalytic promiscuity.
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Affiliation(s)
- Ruishan Wang
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Ridao Chen
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Jianhua Li
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Xiao Liu
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Kebo Xie
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Dawei Chen
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Yunze Yin
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Xiaoyu Tao
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Dan Xie
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Jianhua Zou
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Lin Yang
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Jungui Dai
- From the State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
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Varella MAC, Valentova JV, Pereira KJ, Bussab VSR. Promiscuity is related to masculine and feminine body traits in both men and women: evidence from Brazilian and Czech samples. Behav Processes 2014; 109 Pt A:34-9. [PMID: 25093932 DOI: 10.1016/j.beproc.2014.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/18/2014] [Accepted: 07/18/2014] [Indexed: 11/17/2022]
Abstract
One of the possible explanations for human within-sex variation in promiscuity stems from conditional strategies dependent on the level of body sex-dimorphism. There is some evidence that masculine men and feminine women are more promiscuous than their sex-atypical counterparts, although mixed results persist. Moreover, another line of evidence shows that more promiscuous women are rather sex-atypical. We tested whether diverse sex-dimorphic body measures (2D:4D, WHR/WSR, handgrip strength, and height and weight) influence sociosexual desires, attitudes, promiscuous behavior, and age of first intercourse in a sex-typical or sex-atypical direction. Participants were 185 young adults, 51 men and 54 women from Brazil, and 40 men and 40 women from the Czech Republic. In men stronger handgrip and more feminine 2D:4D predicted higher sociosexual behaviors, desires, and lower age of the first sexual intercourse. While in women, sociosexual desires were predicted by lower handgrip strength and more feminine 2D:4D. It thus seems that it is rather a mixture of masculine and feminine traits in men, and feminine traits in women that increase their sociosexuality. Masculine traits (height) predicting female promiscuous behavior were specific for only one population. In conclusion, a mosaic combination of sex-typical but also sex-atypical independent body traits can lead to higher promiscuity, particularly in men. Limitations, implications, and future directions for research are considered. This article is part of a Special Issue entitled: Neotropical Behaviour.
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Affiliation(s)
- Marco Antonio Correa Varella
- Department of Basic Psychological Processes, Institute of Psychology, University of Brasilia, Campus Darcy Ribeiro, ICC Sul, Sala AT 022/4, CEP 70.910-900 Brasília, DF, Brazil; Department of Experimental Psychology, Institute of Psychology, University of Sao Paulo, Av. Prof. Mello Moraes n°1721, CEP 05508-030, Cidade Universitária, São Paulo, SP, Brazil.
| | - Jaroslava Varella Valentova
- Center for Theoretical Study, Charles University in Prague and The Academy of Sciences of the Czech Republic, Jilska 1, 110 00 Prague 1, Czech Republic.
| | - Kamila Janaina Pereira
- Department of Experimental Psychology, Institute of Psychology, University of Sao Paulo, Av. Prof. Mello Moraes n°1721, CEP 05508-030, Cidade Universitária, São Paulo, SP, Brazil.
| | - Vera Silvia Raad Bussab
- Department of Experimental Psychology, Institute of Psychology, University of Sao Paulo, Av. Prof. Mello Moraes n°1721, CEP 05508-030, Cidade Universitária, São Paulo, SP, Brazil.
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Lathe R, Kotelevtsev Y. Steroid signaling: ligand-binding promiscuity, molecular symmetry, and the need for gating. Steroids 2014; 82:14-22. [PMID: 24462647 DOI: 10.1016/j.steroids.2014.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 12/03/2013] [Accepted: 01/06/2014] [Indexed: 11/28/2022]
Abstract
Steroid/sterol-binding receptors and enzymes are remarkably promiscuous in the range of ligands they can bind to and, in the case of enzymes, modify - raising the question of how specific receptor activation is achieved in vivo. Estrogen receptors (ER) are modulated by 27-hydroxycholesterol and 5α-androstane-3β,17β-diol (Adiol), in addition to estradiol (E2), and respond to diverse small molecules such as bisphenol A. Steroid-modifying enzymes are also highly promiscuous in ligand binding and metabolism. The specificity problem is compounded by the fact that the steroid core (hydrogenated cyclopentophenanthrene ring system) has several planes of symmetry. Ligand binding can be in symmetrical East-West (rotation) and North-South (inversion) orientations. Hydroxysteroid dehydrogenases (HSDs) can modify symmetrical 7 and 11, also 3 and 17/20, positions, exemplified here by yeast 3α,20β-HSD and mammalian 11β-HSD and 17β-HSD enzymes. Faced with promiscuity and symmetry, other strategies are clearly necessary to promote signaling selectivity in vivo. Gating regulates hormone access via enzymes that preferentially inactivate (or activate) a subclass of ligands, thereby governing which ligands gain receptor access - exemplified by 11β-HSD gating cortisol access to the mineralocorticoid receptor, and P450 CYP7B1 gating Adiol access to ER. Counter-intuitively, the specificity of steroid/sterol action is achieved not by intrinsic binding selectivity but by the combination of local metabolism and binding affinity.
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Affiliation(s)
- Richard Lathe
- State University of Pushchino, Prospekt Nauki, Pushchino 142290, Moscow Region, Russia; Pushchino Branch of the Institute of Bio-Organic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia; Pieta Research, PO Box 27069, Edinburgh EH10 5YW, UK.
| | - Yuri Kotelevtsev
- State University of Pushchino, Prospekt Nauki, Pushchino 142290, Moscow Region, Russia; Pushchino Branch of the Institute of Bio-Organic Chemistry, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia; Biomedical Centre for Research Education and Innovation (CREI), Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia; Queens Medical Research Institute, University of Edinburgh, Little France, Edinburgh EH16 4TJ, UK.
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Honaker MT, Acchione M, Zhang W, Mannervik B, Atkins WM. Enzymatic detoxication, conformational selection, and the role of molten globule active sites. J Biol Chem 2013; 288:18599-611. [PMID: 23649628 DOI: 10.1074/jbc.m112.445767] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning "induced fit" versus "conformational selection" has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1-1 (GSTA1-1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1-1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that "local" molten globule behavior optimizes detoxication enzymes.
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Affiliation(s)
- Matthew T Honaker
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, USA
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