1
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Obaha A, Novinec M. Regulation of Peptidase Activity beyond the Active Site in Human Health and Disease. Int J Mol Sci 2023; 24:17120. [PMID: 38069440 PMCID: PMC10707025 DOI: 10.3390/ijms242317120] [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: 11/17/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
This comprehensive review addresses the intricate and multifaceted regulation of peptidase activity in human health and disease, providing a comprehensive investigation that extends well beyond the boundaries of the active site. Our review focuses on multiple mechanisms and highlights the important role of exosites, allosteric sites, and processes involved in zymogen activation. These mechanisms play a central role in shaping the complex world of peptidase function and are promising potential targets for the development of innovative drugs and therapeutic interventions. The review also briefly discusses the influence of glycosaminoglycans and non-inhibitory binding proteins on enzyme activities. Understanding their role may be a crucial factor in the development of therapeutic strategies. By elucidating the intricate web of regulatory mechanisms that control peptidase activity, this review deepens our understanding in this field and provides a roadmap for various strategies to influence and modulate peptidase activity.
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Affiliation(s)
| | - Marko Novinec
- Faculty of Chemistry and Chemical Technology, Department of Chemistry and Biochemistry, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia;
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2
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Giangrieco I, Ciardiello MA, Tamburrini M, Tuppo L, Rafaiani C, Mari A, Alessandri C. Comparative Analysis of the Immune Response and the Clinical Allergic Reaction to Papain-like Cysteine Proteases from Fig, Kiwifruit, Papaya, Pineapple and Mites in an Italian Population. Foods 2023; 12:2852. [PMID: 37569122 PMCID: PMC10417190 DOI: 10.3390/foods12152852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/09/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Several plant papain-like cysteine proteases are exploited by the food, cosmetic, pharmaceutical and textile industries. However, some of these enzymes can cause allergic reactions. In this context, we investigated the frequency of sensitization and allergic reactions to some fruit and/or latex cysteine proteases, which are used as additives by the food industry to improve and modify the quality of their products. The FABER test was used to analyse the patients' sensitization towards five plants and, for comparison, two homologous mite cysteine proteases. In an Italian population of 341 allergic patients, 133 (39%) had IgE specific for at least one of the seven cysteine proteases under investigation. Most of the patients were IgE positive for Der p 1 and/or Der f 1 (96.38%) reported a clinical history suggestive of respiratory allergy to mites, whereas none of the subjects sensitized to the homologs from papaya, pineapple and fig reported allergy symptoms following ingestion of these foods. Only one patient referred symptoms from ingesting kiwifruit. Therefore, the obtained results showed that sensitization to the fruit enzymes was only rarely concomitant with allergic reactions. These observations, together with the literature reports, suggest that the allergy to plant papain-like cysteine proteases might mainly be an occupational disease.
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Affiliation(s)
- Ivana Giangrieco
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 80131 Naples, Italy; (I.G.); (M.T.); (L.T.)
| | - Maria Antonietta Ciardiello
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 80131 Naples, Italy; (I.G.); (M.T.); (L.T.)
| | - Maurizio Tamburrini
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 80131 Naples, Italy; (I.G.); (M.T.); (L.T.)
| | - Lisa Tuppo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 80131 Naples, Italy; (I.G.); (M.T.); (L.T.)
| | - Chiara Rafaiani
- Associated Centers for Molecular Allergology (CAAM), 00100 Rome, Italy; (C.R.); (A.M.); (C.A.)
| | - Adriano Mari
- Associated Centers for Molecular Allergology (CAAM), 00100 Rome, Italy; (C.R.); (A.M.); (C.A.)
- Allergy Data Laboratories (ADL), 04100 Latina, Italy
| | - Claudia Alessandri
- Associated Centers for Molecular Allergology (CAAM), 00100 Rome, Italy; (C.R.); (A.M.); (C.A.)
- Allergy Data Laboratories (ADL), 04100 Latina, Italy
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3
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Sato S, Yamamoto K, Ito M, Nishino K, Otsuka T, Irie K, Nagao M. Enhancement of Inhibitory Activity by Combining Allosteric Inhibitors Putatively Binding to Different Allosteric Sites on Cathepsin K. Molecules 2023; 28:molecules28104197. [PMID: 37241936 DOI: 10.3390/molecules28104197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Cathepsin K, which is involved in bone resorption, is a good target for treating osteoporosis, but no clinically approved medicine has been developed. Recently, allosteric inhibitors with high specificity and few side effects have been attracting attention for use in new medicines. METHODS Cathepsin K inhibitors were isolated from the methanol extract of Chamaecrista nomame (Leguminosae) using cathepsin K inhibition activity-assisted multi-step chromatography. Standard kinetic analysis was employed to examine the mechanism of cathepsin K inhibition when an isolated inhibitor and its derivative were used. The allosteric binding of these cathepsin K inhibitors was supported by a docking study using AutoDock vina. Combinations of allosteric cathepsin K inhibitors expected to bind to different allosteric sites were examined by means of cathepsin K inhibition assay. RESULTS Two types of cathepsin K inhibitors were identified in the methanol extract of Chamaecrista nomame. One type consisted of cassiaoccidentalin B and torachrysone 8-β-gentiobioside, and inhibited both cathepsin K and B with similar inhibitory potential, while the other type of inhibitor consisted of pheophytin a, and inhibited cathepsin K but not cathepsin B, suggesting that pheophytin a binds to an allosteric site of cathepsin K. Kinetic analysis of inhibitory activity suggested that pheophytin a and its derivative, pheophorbide b, bind allosterically to cathepsin K. This possibility was supported by a docking study on cathepsin K. The cathepsin K inhibitory activity of pheophytin a and pheophorbide b was enhanced by combining them with the allosteric inhibitors NSC 13345 and NSC94914, which bind to other allosteric sites on cathepsin K. CONCLUSIONS Different allosteric inhibitors that bind to different sites in combination, as shown in this study, may be useful for designing new allosteric inhibitory drugs with high specificity and few side effects.
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Affiliation(s)
- Shun Sato
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kana Yamamoto
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Moeno Ito
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Takanao Otsuka
- Department of Applied Chemistry and Biotechnology, Okayama University of Science, Okayama 700-0005, Japan
| | - Kazuhiro Irie
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masaya Nagao
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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4
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Govindaraj RG, Thangapandian S, Schauperl M, Denny RA, Diller DJ. Recent applications of computational methods to allosteric drug discovery. Front Mol Biosci 2023; 9:1070328. [PMID: 36710877 PMCID: PMC9877542 DOI: 10.3389/fmolb.2022.1070328] [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: 10/14/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
Interest in exploiting allosteric sites for the development of new therapeutics has grown considerably over the last two decades. The chief driving force behind the interest in allostery for drug discovery stems from the fact that in comparison to orthosteric sites, allosteric sites are less conserved across a protein family, thereby offering greater opportunity for selectivity and ultimately tolerability. While there is significant overlap between structure-based drug design for orthosteric and allosteric sites, allosteric sites offer additional challenges mostly involving the need to better understand protein flexibility and its relationship to protein function. Here we examine the extent to which structure-based drug design is impacting allosteric drug design by highlighting several targets across a variety of target classes.
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Affiliation(s)
- Rajiv Gandhi Govindaraj
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States,*Correspondence: Rajiv Gandhi Govindaraj,
| | | | - Michael Schauperl
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
| | | | - David J. Diller
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
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5
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Kinetic Characterization of Cerium and Gallium Ions as Inhibitors of Cysteine Cathepsins L, K, and S. Int J Mol Sci 2022; 23:ijms23168993. [PMID: 36012257 PMCID: PMC9409168 DOI: 10.3390/ijms23168993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022] Open
Abstract
Heavy metal ions can disrupt biological functions via multiple molecular mechanisms, including inhibition of enzymes. We investigate the interactions of human papain-like cysteine endopeptidases cathepsins L, K, and S with gallium and cerium ions, which are associated with medical applications. We compare these results with zinc and lead, which are known to inhibit thiol enzymes. We show that Ga3+, Ce3+, and Ce4+ ions inhibit all tested peptidases with inhibition constants in the low micromolar range (between 0.5 µM and 10 µM) which is comparable to Zn2+ ions, whereas inhibition constants of Pb2+ ions are one order of magnitude higher (30 µM to 150 µM). All tested ions are linear specific inhibitors of cathepsin L, but cathepsins K and S are inhibited by Ga3+, Ce3+, and Ce4+ ions via hyperbolic inhibition mechanisms. This indicates a mode of interaction different from that of Zn2+ and Pb2+ ions, which act as linear specific inhibitors of all peptidases. All ions also inhibit the degradation of insoluble elastin, which is a common target of these peptidases in various inflammatory diseases. Our results suggest that these ions and their compounds have the potential to be used as cysteine cathepsin inhibitors in vitro and possibly in vivo.
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6
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Bhattacharya S, Palillo A. Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1. Protein Sci 2022; 31:498-512. [PMID: 34865273 PMCID: PMC8820281 DOI: 10.1002/pro.4248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 02/03/2023]
Abstract
The export of antimicrobial peptides is mediated by diverse mechanisms in bacterial quorum sensing pathways. One such binary system employed by gram-positive bacteria is the PCAT1 ABC transporter coupled to a cysteine protease. The focus of this study is the N-terminal C39 peptidase (PEP) domain from Clostridium thermocellum PCAT1 that processes its natural substrate CtA by cleaving a conserved -GG- motif to separate the cargo from the leader peptide prior to secretion. In this study, we are primarily interested in elucidating the dynamic and structural determinants of CtA binding and how it is coupled to cleavage efficiency in the PCAT1 PEP domain. To this end, we have characterized CtA interactions with PEP domain and PCAT1 transporter in detergent micelles using solution nuclear magnetic resonance spectroscopy. The bound CtA structure revealed the disordered C-terminal cargo peptide is linked by a sterically hindered cleavage site to a helix docked within a hydrophobic cavity in the PEP domain. The wide range of internal motions detected by amide nitrogen (N15 ) relaxation measurements in the free enzyme and substrate-bound complex suggests the binding site is relatively floppy. This flexibility plays a key role in the structural rearrangement necessary to relax steric inhibition in the bound substrate. In conjunction with previously reported PCAT1 structures, we offer fresh insight into the ATP-mediated association between PEP and transmembrane domains as a putative mechanism to optimize peptide cleavage by regulating the width and flexibility of the enzyme active site.
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Affiliation(s)
| | - Anthony Palillo
- Laboratory of Membrane Biology and Biophysics, The Rockefeller UniversityNew YorkNew YorkUSA,Joan and Sanford I Weill Medical College of Cornell UniversityNew YorkNew YorkUSA
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7
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Rocha GV, Bastos LS, Costa MGS. Identification of potential allosteric binding sites in cathepsin K based on intramolecular communication. Proteins 2020; 88:1675-1687. [PMID: 32683717 DOI: 10.1002/prot.25985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/02/2020] [Accepted: 07/12/2020] [Indexed: 12/18/2022]
Abstract
Network theory methods and molecular dynamics (MD) simulations are accepted tools to study allosteric regulation. Indeed, dynamic networks built upon correlation analysis of MD trajectories provide detailed information about communication paths between distant sites. In this context, we aimed to understand whether the efficiency of intramolecular communication could be used to predict the allosteric potential of a given site. To this end, we performed MD simulations and network theory analyses in cathepsin K (catK), whose allosteric sites are well defined. To obtain a quantitative measure of the efficiency of communication, we designed a new protocol that enables the comparison between properties related to ensembles of communication paths obtained from different sites. Further, we applied our strategy to evaluate the allosteric potential of different catK cavities not yet considered for drug design. Our predictions of the allosteric potential based on intramolecular communication correlate well with previous catK experimental and theoretical data. We also discuss the possibility of applying our approach to other proteins from the same family.
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Affiliation(s)
- Gisele V Rocha
- Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris Saclay, Centre National de la Recherche Scientifique, Cachan, France
| | - Leonardo S Bastos
- Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Mauricio G S Costa
- Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris Saclay, Centre National de la Recherche Scientifique, Cachan, France
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8
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South African Abietane Diterpenoids and Their Analogs as Potential Antimalarials: Novel Insights from Hybrid Computational Approaches. Molecules 2019; 24:molecules24224036. [PMID: 31703388 PMCID: PMC6891524 DOI: 10.3390/molecules24224036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
The hemoglobin degradation process in Plasmodium parasites is vital for nutrient acquisition required for their growth and proliferation. In P. falciparum, falcipains (FP-2 and FP-3) are the major hemoglobinases, and remain attractive antimalarial drug targets. Other Plasmodium species also possess highly homologous proteins to FP-2 and FP-3. Although several inhibitors have been designed against these proteins, none has been commercialized due to associated toxicity on human cathepsins (Cat-K, Cat-L and Cat-S). Despite the two enzyme groups sharing a common structural fold and catalytic mechanism, distinct active site variations have been identified, and can be exploited for drug development. Here, we utilize in silico approaches to screen 628 compounds from the South African natural sources to identify potential hits that can selectively inhibit the plasmodial proteases. Using docking studies, seven abietane diterpenoids, binding strongly to the plasmodial proteases, and three additional analogs from PubChem were identified. Important residues involved in ligand stabilization were identified for all potential hits through binding pose analysis and their energetic contribution determined by binding free energy calculations. The identified compounds present important scaffolds that could be further developed as plasmodial protease inhibitors. Previous laboratory assays showed the effect of the seven diterpenoids as antimalarials. Here, for the first time, we demonstrate that their possible mechanism of action could be by interacting with falcipains and their plasmodial homologs. Dynamic residue network (DRN) analysis on the plasmodial proteases identified functionally important residues, including a region with high betweenness centrality, which had previously been proposed as a potential allosteric site in FP-2.
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9
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Rebernik M, Snoj T, Klemenčič M, Novinec M. Interplay between tetrameric structure, enzymatic activity and allosteric regulation of human dipeptidyl-peptidase I. Arch Biochem Biophys 2019; 675:108121. [DOI: 10.1016/j.abb.2019.108121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/10/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023]
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10
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Hernández González JE, Hernández Alvarez L, Pascutti PG, Leite VBP. Prediction of Noncompetitive Inhibitor Binding Mode Reveals Promising Site for Allosteric Modulation of Falcipain-2. J Phys Chem B 2019; 123:7327-7342. [DOI: 10.1021/acs.jpcb.9b05021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jorge Enrique Hernández González
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Lilian Hernández Alvarez
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Pedro Geraldo Pascutti
- Laboratório de Dinâmica e Modelagem Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ave. Carlos
Chagas Filho, 373, CCS-Bloco D sala 30, Cidade Universitária
Ilha de Fundão, Rio de Janeiro, CEP 21941-902, Brazil
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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Ferraro F, Merlino A, Gil J, Cerecetto H, Corvo I, Cabrera M. Cathepsin L Inhibitors with Activity against the Liver Fluke Identified From a Focus Library of Quinoxaline 1,4-di- N-Oxide Derivatives. Molecules 2019; 24:molecules24132348. [PMID: 31247891 PMCID: PMC6651555 DOI: 10.3390/molecules24132348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 11/16/2022] Open
Abstract
Infections caused by Fasciola species are widely distributed in cattle and sheep causing significant economic losses, and are emerging as human zoonosis with increasing reports of human cases, especially in children in endemic areas. The current treatment is chemotherapeutic, triclabendazole being the drug of preference since it is active against all parasite stages. Due to the emergence of resistance in several countries, the discovery of new chemical entities with fasciolicidal activity is urgently needed. In our continuous search for new fasciolicide compounds, we identified and characterized six quinoxaline 1,4-di-N-oxide derivatives from our in-house library. We selected them from a screening of novel inhibitors against FhCL1 and FhCL3 proteases, two essential enzymes secreted by juvenile and adult flukes. We report compounds C7, C17, C18, C19, C23, and C24 with an IC50 of less than 10 µM in at least one cathepsin. We studied their binding kinetics in vitro and their enzyme-ligand interactions in silico by molecular docking and molecular dynamic (MD) simulations. These compounds readily kill newly excysted juveniles in vitro and have low cytotoxicity in a Hep-G2 cell line and bovine spermatozoa. Our findings are valuable for the development of new chemotherapeutic approaches against fascioliasis, and other pathologies involving cysteine proteases.
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Affiliation(s)
- Florencia Ferraro
- Laboratorio de I + D de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Alicia Merlino
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Jorge Gil
- Laboratorio de Reproducción Animal, Producción y Reproducción de Rumiantes, Departamento de Ciencias Biológicas, CENUR Litoral Norte-Facultad de Veterinaria, Universidad de la República, Paysandú 60000, Uruguay
| | - Hugo Cerecetto
- Grupo de Química Medicinal, Laboratorio de Química Orgánica & Área de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Ileana Corvo
- Laboratorio de I + D de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay.
| | - Mauricio Cabrera
- Laboratorio de I + D de Moléculas Bioactivas, Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay.
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Perricone U, Gulotta MR, Lombino J, Parrino B, Cascioferro S, Diana P, Cirrincione G, Padova A. An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge. MEDCHEMCOMM 2018; 9:920-936. [PMID: 30108981 PMCID: PMC6072422 DOI: 10.1039/c8md00166a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/19/2018] [Indexed: 12/14/2022]
Abstract
Molecular dynamics (MD) has become increasingly popular due to the development of hardware and software solutions and the improvement in algorithms, which allowed researchers to scale up calculations in order to speed them up. MD simulations are usually used to address protein folding issues or protein-ligand complex stability through energy profile analysis over time. In recent years, the development of new tools able to deeply explore a potential energy surface (PES) has allowed researchers to focus on the dynamic nature of the binding recognition process and binding-induced protein conformational changes. Moreover, modern approaches have been demonstrated to be effective and reliable in calculating some kinetic and thermodynamic parameters behind the host-guest recognition process. Starting from all of these considerations, several efforts have been made in order to integrate MD within the virtual screening process in drug discovery. Knowledge retrieved from MD can, in fact, be exploited as a starting point to build pharmacophores or docking constraints in the early stage of the screening campaign as well as to define key features, in order to unravel hidden binding modes and help the optimisation of the molecular structure of a lead compound. Based on these outcomes, researchers are nowadays using MD as an invaluable tool to discover and target previously considered undruggable binding sites, including protein-protein interactions and allosteric sites on a protein surface. As a matter of fact, the use of MD has been recognised as vital to the discovery of selective protein-protein interaction modulators. The use of a dynamic overview on how the host-guest recognition occurs and of the relative conformational modifications induced allows researchers to optimise small molecules and small peptides capable of tightly interacting within the cleft between two proteins. In this review, we aim to present the most recent applications of MD as an integrated tool to be used in the rational design of small molecules or small peptides able to modulate undruggable targets, such as allosteric sites and protein-protein interactions.
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Affiliation(s)
- Ugo Perricone
- Computational and Medicinal Chemistry Group , Fondazione Ri.MED , Via Bandiera 11 , 90133 Palermo , Italy .
| | - Maria Rita Gulotta
- Computational and Medicinal Chemistry Group , Fondazione Ri.MED , Via Bandiera 11 , 90133 Palermo , Italy .
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Via Archirafi 32 , 90123 Palermo , Italy
| | - Jessica Lombino
- Computational and Medicinal Chemistry Group , Fondazione Ri.MED , Via Bandiera 11 , 90133 Palermo , Italy .
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Via Archirafi 32 , 90123 Palermo , Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Via Archirafi 32 , 90123 Palermo , Italy
| | - Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Via Archirafi 32 , 90123 Palermo , Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Via Archirafi 32 , 90123 Palermo , Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Via Archirafi 32 , 90123 Palermo , Italy
| | - Alessandro Padova
- Computational and Medicinal Chemistry Group , Fondazione Ri.MED , Via Bandiera 11 , 90133 Palermo , Italy .
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Corvo I, Ferraro F, Merlino A, Zuberbühler K, O'Donoghue AJ, Pastro L, Pi-Denis N, Basika T, Roche L, McKerrow JH, Craik CS, Caffrey CR, Tort JF. Substrate Specificity of Cysteine Proteases Beyond the S 2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L. Front Mol Biosci 2018; 5:40. [PMID: 29725596 PMCID: PMC5917446 DOI: 10.3389/fmolb.2018.00040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
Abstract
Cysteine proteases are widespread in all life kingdoms, being central to diverse physiological processes based on a broad range of substrate specificity. Paralogous Fasciola hepatica cathepsin L proteases are essential to parasite invasion, tissue migration and reproduction. In spite of similarities in their overall sequence and structure, these enzymes often exhibit different substrate specificity. These preferences are principally determined by the amino acid composition of the active site's S2 subsite (pocket) of the enzyme that interacts with the substrate P2 residue (Schetcher and Berger nomenclature). Although secreted FhCL1 accommodates aliphatic residues in the S2 pocket, FhCL2 is also efficient in cleaving proline in that position. To understand these differences, we engineered the FhCL1 S2 subsite at three amino acid positions to render it identical to that present in FhCL2. The substitutions did not produce the expected increment in proline accommodation in P2. Rather, they decreased the enzyme's catalytic efficiency toward synthetic peptides. Nonetheless, a change in the P3 specificity was associated with the mutation of Leu67 to Tyr, a hinge residue between the S2 and S3 subsites that contributes to the accommodation of Gly in S3. Molecular dynamic simulations highlighted changes in the spatial distribution and secondary structure of the S2 and S3 pockets of the mutant FhCL1 enzymes. The reduced affinity and catalytic efficiency of the mutant enzymes may be due to a narrowing of the active site cleft that hinders the accommodation of substrates. Because the variations in the enzymatic activity measured could not be exclusively allocated to those residues lining the active site, other more external positions might modulate enzyme conformation, and, therefore, catalytic activity.
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Affiliation(s)
- Ileana Corvo
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Florencia Ferraro
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alicia Merlino
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Kathrin Zuberbühler
- Department of Pharmaceutical Chemistry, Pharmacology, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Lucía Pastro
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Natalia Pi-Denis
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Tatiana Basika
- Departamento de Biología Celular y Molecular, Unidad de Biología Parasitaria, Facultad de Ciencias, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Leda Roche
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - James H McKerrow
- Department of Pathology, Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, CA, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, Pharmacology, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Conor R Caffrey
- Department of Pathology, Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, CA, United States
| | - José F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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