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Ullah S, Rahman W, Ullah F, Ullah A, Jehan R, Iqbal MN, Ali I, Tianshun G. Identification of lead compound screened from the natural products atlas to treat renal inflammasomes using molecular docking and dynamics simulation. J Biomol Struct Dyn 2024; 42:4851-4861. [PMID: 37705295 DOI: 10.1080/07391102.2023.2254397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/04/2023] [Indexed: 09/15/2023]
Abstract
One of the most prevalent ailments is kidney disease. Effective therapies for chronic renal disease are hard to come by. As a result, there is significant clinical and social interest to predict and develop novel compounds to treat renal disorders. So, specific natural products have been employed in this study because they have protective effects against kidney diseases. When taken orally, natural products can help protect against or lessen the severity of the kidney damage caused by high fructose intake, a high-fat diet, and both Type I and Type 2 diabetes. Reduced podocyte injury, a contributor to albuminuria in diabetic nephropathy, reduces renal endothelial barrier function disruption due to hyperglycemia, as well as urinary microalbumin excretion and glomerular hyperfiltration. Multiple natural products have been shown to protect the kidneys from nephrotoxic chemicals such as LPS, gentamycin, alcohol, nicotine, lead, and cadmium, all of which can persuade acute kidney injury (AKI) or chronic kidney disease (CKD). Natural compounds inhibit regulatory enzymes for controlling inflammation-related diseases. For this, use computational methods such as drug design to identify novel flavonoid compounds against kidney diseases. Drug design via computational methods gaining admiration as a swift and effective technique to identify lead compounds in a shorter time at a low cost. In this in-silico study, we screened The Natural Product Atlas based on a structure-based pharmacophore query. Top hits were analyzed for ADMET analysis followed by molecular docking and docking validation. Finally, the lead compound was simulated for a period of 200 ns and trajectories were studied for stability. We found that NPA024823 showed promising binding and stability with the AIM2. This research work aims to predict novel anti-inflammatory compounds against kidney diseases to inhibit kidney inflammasome by targeting the AIM2 protein. So, in initial preclinical research, there will be lower failure rates that demonstrate safety profiles against predicted compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Anees Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Muhammad Nasir Iqbal
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology, and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Gao Tianshun
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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Ahn Y, Park JH. Novel Potential Therapeutic Targets in Autosomal Dominant Polycystic Kidney Disease from the Perspective of Cell Polarity and Fibrosis. Biomol Ther (Seoul) 2024; 32:291-300. [PMID: 38589290 PMCID: PMC11063481 DOI: 10.4062/biomolther.2023.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 04/10/2024] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), a congenital genetic disorder, is a notable contributor to the prevalence of chronic kidney disease worldwide. Despite the absence of a complete cure, ongoing research aims for early diagnosis and treatment. Although agents such as tolvaptan and mTOR inhibitors have been utilized, their effectiveness in managing the disease during its initial phase has certain limitations. This review aimed to explore new targets for the early diagnosis and treatment of ADPKD, considering ongoing developments. We particularly focus on cell polarity, which is a key factor that influences the process and pace of cyst formation. In addition, we aimed to identify agents or treatments that can prevent or impede the progression of renal fibrosis, ultimately slowing its trajectory toward end-stage renal disease. Recent advances in slowing ADPKD progression have been examined, and potential therapeutic approaches targeting multiple pathways have been introduced. This comprehensive review discusses innovative strategies to address the challenges of ADPKD and provides valuable insights into potential avenues for its prevention and treatment.
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Affiliation(s)
- Yejin Ahn
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310, 04310, Republic of Korea
| | - Jong Hoon Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul, 04310, 04310, Republic of Korea
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul, 04310, Republic of Korea
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Khan MAH, Nolan B, Stavniichuk A, Merk D, Imig JD. Dual soluble epoxide hydrolase inhibitor - farnesoid X receptor agonist interventional treatment attenuates renal inflammation and fibrosis. Front Immunol 2024; 14:1269261. [PMID: 38235144 PMCID: PMC10791967 DOI: 10.3389/fimmu.2023.1269261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Introduction Renal fibrosis associated with inflammation is a critical pathophysiological event in chronic kidney disease (CKD). We have developed DM509 which acts concurrently as a farnesoid X receptor agonist and a soluble epoxide hydrolase inhibitor and investigated DM509 efficacy as an interventional treatment using the unilateral ureteral obstruction (UUO) mouse model. Methods Male mice went through either UUO or sham surgery. Interventional DM509 treatment (10mg/kg/d) was started three days after UUO induction and continued for 7 days. Plasma and kidney tissue were collected at the end of the experimental protocol. Results UUO mice demonstrated marked renal fibrosis with higher kidney hydroxyproline content and collagen positive area. Interventional DM509 treatment reduced hydroxyproline content by 41% and collagen positive area by 65%. Renal inflammation was evident in UUO mice with elevated MCP-1, CD45-positive immune cell positive infiltration, and profibrotic inflammatory gene expression. DM509 treatment reduced renal inflammation in UUO mice. Renal fibrosis in UUO was associated with epithelial-to-mesenchymal transition (EMT) and DM509 treatment reduced EMT. UUO mice also had tubular epithelial barrier injury with increased renal KIM-1, NGAL expression. DM509 reduced tubular injury markers by 25-50% and maintained tubular epithelial integrity in UUO mice. Vascular inflammation was evident in UUO mice with 9 to 20-fold higher ICAM and VCAM gene expression which was reduced by 40-50% with DM509 treatment. Peritubular vascular density was reduced by 35% in UUO mice and DM509 prevented vascular loss. Discussion Interventional treatment with DM509 reduced renal fibrosis and inflammation in UUO mice demonstrating that DM509 is a promising drug that combats renal epithelial and vascular pathological events associated with progression of CKD.
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Affiliation(s)
- Md. Abdul Hye Khan
- Drug Discovery Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Benjamin Nolan
- Drug Discovery Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anna Stavniichuk
- Drug Discovery Center, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians Universität München, Munich, Germany
| | - John D. Imig
- Drug Discovery Center, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Imig JD. Peroxisome proliferator-activated receptors, farnesoid X receptor, and dual modulating drugs in hypertension. Front Physiol 2023; 14:1186477. [PMID: 37427406 PMCID: PMC10326315 DOI: 10.3389/fphys.2023.1186477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Abstract
Hypertension characterized by an elevated blood pressure is a cardiovascular disease that afflicts greater than one in every three adults worldwide. Nuclear receptors are large superfamily of DNA-binding transcription factors that target genes to regulate metabolic and cardiovascular function. Drugs have been developed for nuclear receptors such as peroxisome proliferator-activated receptors (PPARα and PPARγ) and farnesoid X receptor (FXR). PPARα, PPARγ, and FXR agonists are used clinically to treat lipid disorders and metabolic diseases. Evidence from clinical studies and animal hypertension models have demonstrated that PPARα, PPARγ, and FXR agonism can lower blood pressure and decrease end organ damage which could be useful for the treatment of hypertension in patients with metabolic diseases. Unfortunately, PPAR and FXR agonists have unwanted clinical side effects. There have been recent developments to limit side effects for PPAR and FXR agonists. Combining PPAR and FXR agonism with soluble epoxide hydrolase (sEH) inhibition or Takeda G protein receptor 5 (TGR5) agonism has been demonstrated in preclinical studies to have actions that would decrease clinical side effects. In addition, these dual modulating drugs have been demonstrated in preclinical studies to have blood pressure lowering, anti-fibrotic, and anti-inflammatory actions. There is now an opportunity to thoroughly test these novel dual modulators in animal models of hypertension associated with metabolic diseases. In particular, these newly developed dual modulating PPAR and FXR drugs could be beneficial for the treatment of metabolic diseases, organ fibrosis, and hypertension.
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Ryszkiewicz P, Malinowska B, Schlicker E. Polypharmacology: promises and new drugs in 2022. Pharmacol Rep 2023:10.1007/s43440-023-00501-4. [PMID: 37278927 PMCID: PMC10243259 DOI: 10.1007/s43440-023-00501-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/20/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023]
Abstract
Polypharmacology is an emerging strategy of design, synthesis, and clinical implementation of pharmaceutical agents that act on multiple targets simultaneously. It should not be mixed up with polytherapy, which is based on the use of multiple selective drugs and is considered a cornerstone of current clinical practice. However, this 'classic' approach, when facing urgent medical challenges, such as multifactorial diseases, increasing resistance to pharmacotherapy, and multimorbidity, seems to be insufficient. The 'novel' polypharmacology concept leads to a more predictable pharmacokinetic profile of multi-target-directed ligands (MTDLs), giving a chance to avoid drug-drug interactions and improve patient compliance due to the simplification of dosing regimens. Plenty of recently marketed drugs interact with multiple biological targets or disease pathways. Many offer a significant additional benefit compared to the standard treatment regimens. In this paper, we will briefly outline the genesis of polypharmacology and its differences to polytherapy. We will also present leading concepts for obtaining MTDLs. Subsequently, we will describe some successfully marketed drugs, the mechanisms of action of which are based on the interaction with multiple targets. To get an idea, of whether MTDLs are indeed important in contemporary pharmacology, we also carefully analyzed drugs approved in 2022 in Germany: 10 out of them were found multi-targeting, including 7 antitumor agents, 1 antidepressant, 1 hypnotic, and 1 drug indicated for eye disease.
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Affiliation(s)
- Piotr Ryszkiewicz
- Department of Experimental Physiology and Pathophysiology, Medical University of Bialystok, 15-222, Bialystok, Poland
| | - Barbara Malinowska
- Department of Experimental Physiology and Pathophysiology, Medical University of Bialystok, 15-222, Bialystok, Poland.
| | - Eberhard Schlicker
- Department of Pharmacology and Toxicology, University of Bonn, 53127, Bonn, Germany.
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Ni WJ, Lu H, Ma NN, Hou BB, Zeng J, Zhou H, Shao W, Meng XM. RNA N 6 -methyladenosine modifications and potential targeted therapeutic strategies in kidney disease. Br J Pharmacol 2023; 180:5-24. [PMID: 36196023 DOI: 10.1111/bph.15968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 09/13/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modifications have received increasing attention and have been shown to be extensively involved in kidney development and disease progression. Among them, the most common RNA modification, N6 -methyladenosine (m6 A), has been shown to dynamically and reversibly exert its functions in multiple ways, including splicing, export, decay and translation initiation efficiency to regulate mRNA fate. Moreover, m6 A has also been reported to exert biological effects by destabilizing base pairing to modulate various functions of RNAs. Most importantly, an increasing number of kidney diseases, such as renal cell carcinoma, acute kidney injury and chronic kidney disease, have been found to be associated with aberrant m6 A patterns. In this review, we comprehensively review the critical roles of m6 A in kidney diseases and discuss the possibilities and relevance of m6 A-targeted epigenetic therapy, with an integrated comprehensive description of the detailed alterations in specific loci that contribute to cellular processes that are associated with kidney diseases.
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Affiliation(s)
- Wei-Jian Ni
- Department of Pharmacy, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China.,Anhui Provincial Hospital, Anhui Medical University, Hefei, Anhui, 230001, China
| | - Hao Lu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Nan-Nan Ma
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230601, China
| | - Bing-Bing Hou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
| | - Jing Zeng
- Anhui Provincial Hospital, Anhui Medical University, Hefei, Anhui, 230001, China
| | - Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Wei Shao
- School of Basic Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
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Kandeel M, Iqbal MN, Ali I, Malik S, Malik A, Sehgal SA. Comprehensive in silico analyses of flavonoids elucidating the drug properties against kidney disease by targeting AIM2. PLoS One 2023; 18:e0285965. [PMID: 37200367 DOI: 10.1371/journal.pone.0285965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023] Open
Abstract
Kidney disorders are among the most common diseases and there is a scarcity of effective treatments for chronic kidney disease. There has been a progressive improvement in specific flavonoids for protective effects against kidney diseases. Flavonoids inhibit the regulatory enzymes to control inflammation-related diseases. In the present study, a hybrid approach of molecular docking analyses and molecular dynamic simulation was followed by principal component analyses and a dynamics cross-correlation matrix. In the present study, the top-ranked five flavonoids were reported, and the maximum binding affinity was observed against AIM2. Molecular docking analyses revealed that Glu_186, Phe_187, Lys_245, Glu_248, Ile_263, and Asn_265 are potent residues against AIM2 for ligand-receptor interactions. Extensive in silico analyses suggested that procyanidin is a potential molecule against AIM2. Moreover, the site-directed mutagenesis for the reported interacting residues of AIM2 could be important for further in vitro analyses. The observed novel results based on extensive computational analyses may be significant for potential drug design against renal disorders by targeting AIM2.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
| | - Muhammad Nasir Iqbal
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad, Pakistan
| | - Saima Malik
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abbeha Malik
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Department of Bioinformatics, University of Okara, Okara, Pakistan
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Metabolic mechanisms of acute proximal tubular injury. Pflugers Arch 2022; 474:813-827. [PMID: 35567641 PMCID: PMC9338906 DOI: 10.1007/s00424-022-02701-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/12/2022] [Accepted: 05/02/2022] [Indexed: 12/11/2022]
Abstract
Damage to the proximal tubule (PT) is the most frequent cause of acute kidney injury (AKI) in humans. Diagnostic and treatment options for AKI are currently limited, and a deeper understanding of pathogenic mechanisms at a cellular level is required to rectify this situation. Metabolism in the PT is complex and closely coupled to solute transport function. Recent studies have shown that major changes in PT metabolism occur during AKI and have highlighted some potential targets for intervention. However, translating these insights into effective new therapies still represents a substantial challenge. In this article, in addition to providing a brief overview of the current state of the field, we will highlight three emerging areas that we feel are worthy of greater attention. First, we will discuss the role of axial heterogeneity in cellular function along the PT in determining baseline susceptibility to different metabolic hits. Second, we will emphasize that elucidating insult specific pathogenic mechanisms will likely be critical in devising more personalized treatments for AKI. Finally, we will argue that uncovering links between tubular metabolism and whole-body homeostasis will identify new strategies to try to reduce the considerable morbidity and mortality associated with AKI. These concepts will be illustrated by examples of recent studies emanating from the authors' laboratories and performed under the auspices of the Swiss National Competence Center for Kidney Research (NCCR Kidney.ch).
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