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Gómez-García A, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, Bolzani VDS, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Valencia Sánchez HA, Cortés Hernández HF, Medina-Franco JL. Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals (Basel) 2023; 16:1388. [PMID: 37895859 PMCID: PMC10609821 DOI: 10.3390/ph16101388] [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: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.
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Affiliation(s)
- Alejandro Gómez-García
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
| | - Daniel A. Acuña Jiménez
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
| | - William J. Zamora
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José 1174-1200, Costa Rica
| | - Haruna L. Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Miguel Á. Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Adriano D. Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Vanderlan da S. Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, Araraquara 14800-900, SP, Brazil;
| | - Dionisio A. Olmedo
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Pablo N. Solís
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Marvin J. Núñez
- Natural Product Research Laboratory, School of Chemistry and Pharmacy, University of El Salvador, Final Ave. Mártires Estudiantes del 30 de Julio, San Salvador 01101, El Salvador;
| | - Johny R. Rodríguez Pérez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
- GIEPRONAL Research Group, School of Basic Sciences, Technology and Engineering, Universidad Nacional Abierta y a Distancia, Dosquebradas 661001, Colombia
| | - Hoover A. Valencia Sánchez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - Héctor F. Cortés Hernández
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
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Mahajan PS, Girigosavi P, Chauware V, Mokashi ND, Nema V. Issues with the current drugs for Mycobacterium tuberculosis cure and potential of cell envelope proteins for new drug discovery. Indian J Tuberc 2023; 70:286-296. [PMID: 37562902 DOI: 10.1016/j.ijtb.2023.03.015] [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: 06/10/2022] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 08/12/2023]
Abstract
Mycobacterium tuberculosis has been the smartest pathogen ever and a challenge to drug development. Its replicative machinery is unique, so targeting the same for killing the pathogen remains a challenge. Our body typically throws out the drugs before they see the bacterium multiply. The pathogen has also learned how to remove drugs from its internal chambers and not allow them to reach their targets. Another strategy for Mtb is the mutation of the targets to reject drug binding and bypass the drug's inhibitory actions. In this review, we tried to explore possible targets on the outer side of the bacterial cell. We have also explored if those targets are promising enough and if there are drugs or inhibitors available. We also discuss the essential proteins and why they remain to be a good target. We concluded that the cell envelope has got a few proteins that can be targeted in isolation or maybe along with other machinery while making the outer environment more conducive for penetration of current drugs or newly proposed drugs.
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Affiliation(s)
- Pratik S Mahajan
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Payal Girigosavi
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Vijay Chauware
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India
| | - Nitin D Mokashi
- Postgraduate Institute, Yashwantrao Chavan Memorial Hospital, Pune, 411018, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, 411026, India.
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Barazorda-Ccahuana HL, Ranilla LG, Candia-Puma MA, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Davila-Del-Carpio G, Medina-Franco JL, Chávez-Fumagalli MA. PeruNPDB: the Peruvian Natural Products Database for in silico drug screening. Sci Rep 2023; 13:7577. [PMID: 37165197 PMCID: PMC10170056 DOI: 10.1038/s41598-023-34729-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023] Open
Abstract
Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discovery development. For this reason, several countries such as Mexico, Brazil, India, and China have initiatives to assemble and maintain NPs databases that are representative of their diversity and ethnopharmacological usage. We describe the assembly, curation, and chemoinformatic evaluation of the content and coverage in chemical space, as well as the physicochemical attributes and chemical diversity of the initial version of the Peruvian Natural Products Database (PeruNPDB), which contains 280 natural products. Access to PeruNPDB is available for free ( https://perunpdb.com.pe/ ). The PeruNPDB's collection is intended to be used in a variety of tasks, such as virtual screening campaigns against various disease targets or biological endpoints. This emphasizes the significance of biodiversity protection both directly and indirectly on human health.
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Affiliation(s)
- Haruna L Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Lena Gálvez Ranilla
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
- Escuela Profesional de Ingeniería de Industria Alimentaria, Facultad de Ciencias e Ingenierías Biológicas y Químicas, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
| | - Mayron Antonio Candia-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Gonzalo Davila-Del-Carpio
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru.
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Progress and Impact of Latin American Natural Product Databases. Biomolecules 2022; 12:biom12091202. [PMID: 36139041 PMCID: PMC9496143 DOI: 10.3390/biom12091202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug design (CADD) has contributed to drug discovery research, mitigating costs and time. In this sense, compound databases represent a fundamental element of CADD. This work reviews the progress toward developing compound databases of natural origin, and it surveys computational methods, emphasizing chemoinformatic approaches to profile natural product databases. Furthermore, it reviews the present state of the art in developing Latin American NP databases and their practical applications to the drug discovery area.
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Vieira TF, Martins FG, Moreira JP, Barbosa T, Sousa SF. In Silico Identification of Possible Inhibitors for Protein Kinase B (PknB) of Mycobacterium tuberculosis. Molecules 2021; 26:molecules26206162. [PMID: 34684743 PMCID: PMC8541300 DOI: 10.3390/molecules26206162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/18/2023] Open
Abstract
With tuberculosis still being one of leading causes of death in the world and the emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb), researchers have been seeking to find further therapeutic strategies or more specific molecular targets. PknB is one of the 11 Ser/Thr protein kinases of Mtb and is responsible for phosphorylation-mediated signaling, mainly involved in cell wall synthesis, cell division and metabolism. With the amount of structural information available and the great interest in protein kinases, PknB has become an attractive target for drug development. This work describes the optimization and application of an in silico computational protocol to find new PknB inhibitors. This multi-level computational approach combines protein–ligand docking, structure-based virtual screening, molecular dynamics simulations and free energy calculations. The optimized protocol was applied to screen a large dataset containing 129,650 molecules, obtained from the ZINC/FDA-Approved database, Mu.Ta.Lig Virtual Chemotheca and Chimiothèque Nationale. It was observed that the most promising compounds selected occupy the adenine-binding pocket in PknB, and the main interacting residues are Leu17, Val26, Tyr94 and Met155. Only one of the compounds was able to move the active site residues into an open conformation. It was also observed that the P-loop and magnesium position loops change according to the characteristics of the ligand. This protocol led to the identification of six compounds for further experimental testing while also providing additional structural information for the design of more specific and more effective derivatives.
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Affiliation(s)
- Tatiana F. Vieira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Fábio G. Martins
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Joel P. Moreira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Tiago Barbosa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Sérgio F. Sousa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (T.F.V.); (F.G.M.); (J.P.M.); (T.B.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM-Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Correspondence:
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