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Castillo-Campos L, Velázquez-Libera JL, Caballero J. Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2023; 10:1215499. [PMID: 37426421 PMCID: PMC10326900 DOI: 10.3389/fmolb.2023.1215499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
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Ramlal A, Bhat I, Nautiyal A, Baweja P, Mehta S, Kumar V, Tripathi S, Mahto RK, Saini M, Mallikarjuna BP, Saluja S, Lal SK, Subramaniam S, Fawzy IM, Rajendran A. In silico analysis of angiotensin-converting enzyme inhibitory compounds obtained from soybean [ Glycine max (L.) Merr.]. Front Physiol 2023; 14:1172684. [PMID: 37324400 PMCID: PMC10264776 DOI: 10.3389/fphys.2023.1172684] [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: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Cardiovascular diseases (CVDs) are one of the major reasons for deaths globally. The renin-angiotensin-aldosterone system (RAAS) regulates body hypertension and fluid balance which causes CVD. Angiotensin-converting enzyme I (ACE I) is the central Zn-metallopeptidase component of the RAAS playing a crucial role in maintaining homeostasis of the cardiovascular system. The available drugs to treat CVD have many side effects, and thus, there is a need to explore phytocompounds and peptides to be utilized as alternative therapies. Soybean is a unique legume cum oilseed crop with an enriched source of proteins. Soybean extracts serve as a primary ingredient in many drug formulations against diabetes, obesity, and spinal cord-related disorders. Soy proteins and their products act against ACE I which may provide a new scope for the identification of potential scaffolds that can help in the design of safer and natural cardiovascular therapies. In this study, the molecular basis for selective inhibition of 34 soy phytomolecules (especially of beta-sitosterol, soyasaponin I, soyasaponin II, soyasaponin II methyl ester, dehydrosoyasaponin I, and phytic acid) was evaluated using in silico molecular docking approaches and dynamic simulations. Our results indicate that amongst the compounds, beta-sitosterol exhibited a potential inhibitory action against ACE I.
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Affiliation(s)
- Ayyagari Ramlal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, Penang, Malaysia
| | - Isha Bhat
- Department of Biosciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Aparna Nautiyal
- Department of Botany, Deshbandhu College, University of Delhi, New Delhi, India
| | - Pooja Baweja
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Sahil Mehta
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Vikash Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences and Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Shikha Tripathi
- ICAR- National Institute for Biotechnology, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Rohit Kumar Mahto
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Bingi Pujari Mallikarjuna
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), Regional Research Centre, Dharwad, Karnataka, India
| | - Shukla Saluja
- Department of Botany, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - S. K. Lal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Sreeramanan Subramaniam
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, Penang, Malaysia
- Chemical Centre Biology (CCB), Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
- Institute of Nano Optoelectronics Research and Technology, Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
| | - Iten M. Fawzy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt, Cairo, Egypt
| | - Ambika Rajendran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
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Ramlal A, Nautiyal A, Baweja P, Kumar V, Mehta S, Mahto RK, Tripathi S, Shanmugam A, Pujari Mallikarjuna B, Raman P, Lal SK, Raju D, Rajendran A. Angiotensin-converting enzyme inhibitory peptides and isoflavonoids from soybean [ Glycine max (L.) Merr.]. Front Nutr 2022; 9:1068388. [PMID: 36505231 PMCID: PMC9730416 DOI: 10.3389/fnut.2022.1068388] [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: 10/12/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Angiotensin-converting enzyme I (ACE I) is a zinc-containing metallopeptidase involved in the renin-angiotensin system (RAAS) that helps in the regulation of hypertension and maintains fluid balance otherwise, which results in cardiovascular diseases (CVDs). One of the leading reasons of global deaths is due to CVDs. RAAS also plays a central role in maintaining homeostasis of the CV system. The commercial drugs available to treat CVDs possess several fatal side effects. Hence, phytochemicals like peptides having plant-based origin should be explored and utilized as alternative therapies. Soybean is an important leguminous crop that simultaneously possesses medicinal properties. Soybean extracts are used in many drug formulations for treating diabetes and other disorders and ailments. Soy proteins and its edible products such as tofu have shown potential inhibitory activity against ACE. Thus, this review briefly describes various soy proteins and products that can be used to inhibit ACE thereby providing new scope for the identification of potential candidates that can help in the design of safer and natural treatments for CVDs.
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Affiliation(s)
- Ayyagari Ramlal
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Aparna Nautiyal
- Department of Botany, Deshbandhu College, University of Delhi, New Delhi, India
| | - Pooja Baweja
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Vikash Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences and Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Sahil Mehta
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Rohit Kumar Mahto
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), New Delhi, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Shikha Tripathi
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology (NIPB), New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Aravindam Shanmugam
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Bingi Pujari Mallikarjuna
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), Regional Research Centre, Dharwad, Karnataka, India
| | - Pushpa Raman
- Department of Plant Breeding and Genetics, Tamil Nadu Rice Research Institute, Tamil Nadu Agricultural University, Aduthurai, Tamil Nadu, India
| | - S. K. Lal
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Dhandapani Raju
- Division of Plant Physiology, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Ambika Rajendran
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), New Delhi, India
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Zheng W, Tian E, Liu Z, Zhou C, Yang P, Tian K, Liao W, Li J, Ren C. Small molecule angiotensin converting enzyme inhibitors: A medicinal chemistry perspective. Front Pharmacol 2022; 13:968104. [PMID: 36386190 PMCID: PMC9664202 DOI: 10.3389/fphar.2022.968104] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/17/2022] [Indexed: 10/07/2023] Open
Abstract
Angiotensin-converting enzyme (ACE), a zinc metalloprotein, is a central component of the renin-angiotensin system (RAS). It degrades bradykinin and other vasoactive peptides. Angiotensin-converting-enzyme inhibitors (ACE inhibitors, ACEIs) decrease the formation of angiotensin II and increase the level of bradykinin, thus relaxing blood vessels as well as reducing blood volume, lowering blood pressure and reducing oxygen consumption by the heart, which can be used to prevent and treat cardiovascular diseases and kidney diseases. Nevertheless, ACEIs are associated with a range of adverse effects such as renal insufficiency, which limits their use. In recent years, researchers have attempted to reduce the adverse effects of ACEIs by improving the selectivity of ACEIs for structural domains based on conformational relationships, and have developed a series of novel ACEIs. In this review, we have summarized the research advances of ACE inhibitors, focusing on the development sources, design strategies and analysis of structure-activity relationships and the biological activities of ACE inhibitors.
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Affiliation(s)
- Wenyue Zheng
- Departments of Obstetrics & Gynecology and Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Health Management Center, West China Second University Hospital, Chengdu, China
| | - Erkang Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhen Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Changhan Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Pei Yang
- Departments of Obstetrics & Gynecology and Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Health Management Center, West China Second University Hospital, Chengdu, China
| | - Keyue Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wen Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Juan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People’s Hospital, Chengdu, China
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Abstract
INTRODUCTION Molecular docking has been consolidated as one of the most important methods in the molecular modeling field. It has been recognized as a prominent tool in the study of protein-ligand complexes, to describe intermolecular interactions, to accurately predict poses of multiple ligands, to discover novel promising bioactive compounds. Molecular docking methods have evolved in terms of their accuracy and reliability; but there are pending issues to solve for improving the connection between the docking results and the experimental evidence. AREAS COVERED In this article, the author reviews very recent innovative molecular docking applications with special emphasis on reverse docking, treatment of protein flexibility, the use of experimental data to guide the selection of docking poses, the application of Quantum mechanics(QM) in docking, and covalent docking. EXPERT OPINION There are several issues being worked on in recent years that will lead to important breakthroughs in molecular docking methods in the near future These developments are related to more efficient exploration of large datasets and receptor conformations, advances in electronic description, and the use of structural information for guiding the selection of results.
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Affiliation(s)
- Julio Caballero
- Departamento De Bioinformática, Centro De Bioinformática, Simulación Y Modelado (CBSM), Facultad De Ingeniería, Universidad De Talca, Talca, Chile
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Velázquez-Libera JL, Durán-Verdugo F, Valdés-Jiménez A, Núñez-Vivanco G, Caballero J. LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking. Bioinformatics 2020; 36:2912-2914. [PMID: 31926012 DOI: 10.1093/bioinformatics/btaa018] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/27/2019] [Accepted: 01/07/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Root mean square deviation (RMSD) is one of the most useful and straightforward features for structural comparison between different conformations of the same molecule. Commonly, protein-ligand docking programs have included some utilities that allow the calculation of this value; however, they only work efficiently when exists a complete atom label equivalence between the evaluated conformations. RESULTS We present LigRMSD, a free web-server for the automatic matching and RMSD calculations among identical or similar chemical compounds. This server allows the user to submit only a pair of identical or similar molecules or dataset of similar compounds to compare their three-dimensional conformations. AVAILABILITY AND IMPLEMENTATION LigRMSD can be freely accessed at https://ligrmsd.appsbio.utalca.cl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Fabio Durán-Verdugo
- Center for Bioinformatics, Simulations and Modelling, Universidad de Talca, Talca 3460000, Chile
| | - Alejandro Valdés-Jiménez
- Center for Bioinformatics, Simulations and Modelling, Universidad de Talca, Talca 3460000, Chile.,Computer Architecture Department, Universitat Politécnica de Catalunya, Barcelona 08034, Spain
| | - Gabriel Núñez-Vivanco
- Center for Bioinformatics, Simulations and Modelling, Universidad de Talca, Talca 3460000, Chile
| | - Julio Caballero
- Center for Bioinformatics, Simulations and Modelling, Universidad de Talca, Talca 3460000, Chile
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Alfaro S, Navarro-Retamal C, Caballero J. Transforming Non-Selective Angiotensin-Converting Enzyme Inhibitors in C- and N-domain Selective Inhibitors by Using Computational Tools. Mini Rev Med Chem 2020; 20:1436-1446. [DOI: 10.2174/1389557520666191224113830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023]
Abstract
The two-domain dipeptidylcarboxypeptidase Angiotensin-I-converting enzyme (EC
3.4.15.1; ACE) plays an important physiological role in blood pressure regulation via the reninangiotensin
and kallikrein-kinin systems by converting angiotensin I to the potent vasoconstrictor angiotensin
II, and by cleaving a number of other substrates including the vasodilator bradykinin and the
anti-inflammatory peptide N-acetyl-SDKP. Therefore, the design of ACE inhibitors is within the priorities
of modern medical sciences for treating hypertension, heart failures, myocardial infarction, and
other related diseases. Despite the success of ACE inhibitors for the treatment of hypertension and
congestive heart failure, they have some adverse effects, which could be attenuated by selective domain
inhibition. Crystal structures of both ACE domains (nACE and cACE) reported over the last decades
could facilitate the rational drug design of selective inhibitors. In this review, we refer to the history
of the discovery of ACE inhibitors, which has been strongly related to the development of molecular
modeling methods. We stated that the design of novel selective ACE inhibitors is a challenge
for current researchers which requires a thorough understanding of the structure of both ACE domains
and the help of molecular modeling methodologies. Finally, we performed a theoretical design of potential
selective derivatives of trandolaprilat, a drug approved to treat critical conditions of hypertension,
to illustrate how to use molecular modeling methods such as de novo design, docking, Molecular
Dynamics (MD) simulations, and free energy calculations for creating novel potential drugs with specific
interactions inside nACE and cACE binding sites.
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Affiliation(s)
- Sergio Alfaro
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Carlos Navarro-Retamal
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
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Sharma U, Cozier GE, Sturrock ED, Acharya KR. Molecular Basis for Omapatrilat and Sampatrilat Binding to Neprilysin-Implications for Dual Inhibitor Design with Angiotensin-Converting Enzyme. J Med Chem 2020; 63:5488-5500. [PMID: 32337993 PMCID: PMC7304895 DOI: 10.1021/acs.jmedchem.0c00441] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Neprilysin
(NEP) and angiotensin-converting enzyme (ACE) are two
key zinc-dependent metallopeptidases in the natriuretic peptide and
kinin systems and renin–angiotensin–aldosterone system,
respectively. They play an important role in blood pressure regulation
and reducing the risk of heart failure. Vasopeptidase inhibitors omapatrilat
and sampatrilat possess dual activity against these enzymes by blocking
the ACE-dependent conversion of angiotensin I to the potent vasoconstrictor
angiotensin II while simultaneously halting the NEP-dependent degradation
of vasodilator atrial natriuretic peptide. Here, we report crystal
structures of omapatrilat, sampatrilat, and sampatrilat-ASP (a sampatrilat
analogue) in complex with NEP at 1.75, 2.65, and 2.6 Å, respectively.
A detailed analysis of these structures and the corresponding structures
of ACE with these inhibitors has provided the molecular basis of dual
inhibitor recognition involving the catalytic site in both enzymes.
This new information will be very useful in the design of safer and
more selective vasopeptidase inhibitors of NEP and ACE for effective
treatment in hypertension and heart failure.
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Affiliation(s)
- Urvashi Sharma
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Gyles E Cozier
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Edward D Sturrock
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, 7935 Cape Town, Republic of South Africa
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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Evaluating the benefits of renin-angiotensin system inhibitors as cancer treatments. Pharmacol Ther 2020; 211:107527. [PMID: 32173557 DOI: 10.1016/j.pharmthera.2020.107527] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/08/2020] [Indexed: 02/07/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most diverse group of cellular membrane receptors identified and characterized. It is estimated that 30 to 50% of marketed drugs target these receptors. The angiotensin II receptor type 1 (AT1R) is a GPCR which signals in response to systemic alterations of the peptide hormone angiotensin II (AngII) in circulation. The enzyme responsible for converting AngI to AngII is the angiotensin-converting enzyme (ACE). Specific inhibitors for the AT1R (more commonly known as AT1R blockers or antagonists) and ACE are well characterized for their effects on the cardiovascular system. Combined with the extensive clinical data available on patient tolerance of AT1R blockers (ARBs) and ACE inhibitors (ACEIs), as well as their non-classical roles in cancer, the notion of repurposing this class of medications as cancer treatment(s) is explored in the current review. Given that AngII-dependent AT1R activity directly regulates angiogenesis, remodeling of vasculature, pro-inflammatory responses, stem cell programming and hematopoiesis, and electrolyte balance; the modulation of these processes with pharmacologically well characterized medications could present a valuable complementary treatment option for cancer patients.
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Caballero J. Considerations for Docking of Selective Angiotensin-Converting Enzyme Inhibitors. Molecules 2020; 25:molecules25020295. [PMID: 31940798 PMCID: PMC7024173 DOI: 10.3390/molecules25020295] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/30/2023] Open
Abstract
The angiotensin-converting enzyme (ACE) is a two-domain dipeptidylcarboxypeptidase, which has a direct involvement in the control of blood pressure by performing the hydrolysis of angiotensin I to produce angiotensin II. At the same time, ACE hydrolyzes other substrates such as the vasodilator peptide bradykinin and the anti-inflammatory peptide N-acetyl-SDKP. In this sense, ACE inhibitors are bioactive substances with potential use as medicinal products for treatment or prevention of hypertension, heart failures, myocardial infarction, and other important diseases. This review examined the most recent literature reporting ACE inhibitors with the help of molecular modeling. The examples exposed here demonstrate that molecular modeling methods, including docking, molecular dynamics (MD) simulations, quantitative structure-activity relationship (QSAR), etc, are essential for a complete structural picture of the mode of action of ACE inhibitors, where molecular docking has a key role. Examples show that too many works identified ACE inhibitory activities of natural peptides and peptides obtained from hydrolysates. In addition, other works report non-peptide compounds extracted from natural sources and synthetic compounds. In all these cases, molecular docking was used to provide explanation of the chemical interactions between inhibitors and the ACE binding sites. For docking applications, most of the examples exposed here do not consider that: (i) ACE has two domains (nACE and cACE) with available X-ray structures, which are relevant for the design of selective inhibitors, and (ii) nACE and cACE binding sites have large dimensions, which leads to non-reliable solutions during docking calculations. In support of the solution of these problems, the structural information found in Protein Data Bank (PDB) was used to perform an interaction fingerprints (IFPs) analysis applied on both nACE and cACE domains. This analysis provides plots that identify the chemical interactions between ligands and both ACE binding sites, which can be used to guide docking experiments in the search of selective natural components or novel drugs. In addition, the use of hydrogen bond constraints in the S2 and S2′ subsites of nACE and cACE are suggested to guarantee that docking solutions are reliable.
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Affiliation(s)
- Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
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11
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Polakovičová M, Jampílek J. Advances in Structural Biology of ACE and Development of Domain Selective ACE-inhibitors. Med Chem 2019; 15:574-587. [PMID: 31084594 DOI: 10.2174/1573406415666190514081132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/19/2019] [Accepted: 04/28/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND The Angiotensin-I converting enzyme (ACE) is one of the most important components of the renin-angiotensin-aldosterone system controlling blood pressure and renal functions. Inhibitors of ACE are first line therapeutics used in the treatment of hypertension and related cardiovascular diseases. Somatic ACE consists of two homologous catalytic domains, the C- and N-domains. Recent findings have shown that although both domains are highly homologous in structure, they may have different physiological functions. The C-domain is primarily involved in the control of blood pressure, in contrast to the N-domain that is engaged in the regulation of hematopoietic stem cell proliferation. The currently available ACE inhibitors have some adverse effects that can be attributed to the non-selective inhibition of both domains. In addition, specific Ndomain inhibitors have emerged as potential antifibrotic drugs. Therefore, ACE is still an important drug target for the development of novel domain-selective drugs not only for the cardiovascular system but also for other systems. OBJECTIVE Detailed structural information about interactions in the protein-ligand complex is crucial for rational drug design. This review highlights the structural information available from crystallographic data which is essential for the development of domain selective inhibitors of ACE. METHODS Over eighty crystal complexes of ACE are placed into the Protein Database. An overview of X-ray ACE complexes with various inhibitors in C- and N-domains and an analysis of their binding mode have given mechanistic explanation of the structural determinants of selective ligand binding. In addition, ACE domain selective inhibitors with dual modes of action in complexes with ACE are also discussed. CONCLUSION Selectivity of ACE inhibitors for the N- and C-domain is controlled by subtle differences in the amino-acids forming the active site. Reported studies of crystal complexes of inhibitors in the C- and N-domains revealed that most selective inhibitors interact with non-conserved amino-acids between domains and have distinct interactions with the residues in the S2 and S2' subsites of the ACE catalytic site. Moreover, unusual binding of the second molecule of inhibitors in the binding cavity opens new possibilities of exploiting more distant regions of the catalytic center in structure-based design of novel drugs.
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Affiliation(s)
- Mája Polakovičová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-83232 Bratislava, Slovakia
| | - Josef Jampílek
- Division of Biologically Active Complexes and Molecular Magnets, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University Olomouc, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic.,Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, SK-84215 Bratislava, Slovakia
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12
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Cozier GE, Schwager SL, Sharma RK, Chibale K, Sturrock ED, Acharya KR. Crystal structures of sampatrilat and sampatrilat-Asp in complex with human ACE - a molecular basis for domain selectivity. FEBS J 2018; 285:1477-1490. [PMID: 29476645 PMCID: PMC5947662 DOI: 10.1111/febs.14421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/18/2018] [Accepted: 02/20/2018] [Indexed: 11/28/2022]
Abstract
Angiotensin‐1‐converting enzyme (ACE) is a zinc metallopeptidase that consists of two homologous catalytic domains (known as nACE and cACE) with different substrate specificities. Based on kinetic studies it was previously reported that sampatrilat, a tight‐binding inhibitor of ACE, Ki = 13.8 nm and 171.9 nm for cACE and nACE respectively [Sharma et al., Journal of Chemical Information and Modeling (2016), 56, 2486–2494], was 12.4‐fold more selective for cACE. In addition, samAsp, in which an aspartate group replaces the sampatrilat lysine, was found to be a nonspecific and lower micromolar affinity inhibitor. Here, we report a detailed three‐dimensional structural analysis of sampatrilat and samAsp binding to ACE using high‐resolution crystal structures elucidated by X‐ray crystallography, which provides a molecular basis for differences in inhibitor affinity and selectivity for nACE and cACE. The structures show that the specificity of sampatrilat can be explained by increased hydrophobic interactions and a H‐bond from Glu403 of cACE with the lysine side chain of sampatrilat that are not observed in nACE. In addition, the structures clearly show a significantly greater number of hydrophilic and hydrophobic interactions with sampatrilat compared to samAsp in both cACE and nACE consistent with the difference in affinities. Our findings provide new experimental insights into ligand binding at the active site pockets that are important for the design of highly specific domain selective inhibitors of ACE. Database The atomic coordinates and structure factors for N‐ and C‐domains of ACE bound to sampatrilat and sampatrilat‐Asp complexes (6F9V, 6F9R, 6F9T and 6F9U respectively) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).
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Affiliation(s)
- Gyles E Cozier
- Department of Biology and Biochemistry, University of Bath, UK
| | - Sylva L Schwager
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Rajni K Sharma
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Kelly Chibale
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Edward D Sturrock
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, UK
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