Patents on Endophytic Fungi Related to Secondary Metabolites and Biotransformation Applications.

Endophytic fungi are an important group of microorganisms and one of the least studied. They enhance their host's resistance against abiotic stress, disease, insects, pathogens and mammalian herbivores by producing secondary metabolites with a wide spectrum of biological activity. Therefore, they could be an alternative source of secondary metabolites for applications in medicine, pharmacy and agriculture. In this review, we analyzed patents related to the production of secondary metabolites and biotransformation processes through endophytic fungi and their fields of application. We examined 245 patents (224 related to secondary metabolite production and 21 for biotransformation). The most patented fungi in the development of these applications belong to the Aspergillus, Fusarium, Trichoderma, Penicillium, and Phomopsis genera and cover uses in the biomedicine, agriculture, food, and biotechnology industries.

1. Introduction

The term endophyte refers to any organism (bacteria or fungi) that lives in the internal tissues of a host. This endophyte–host association is complex: it is normally driven without causing harm or apparent disease symptoms and provides benefits in survival, fitness, biodiversity, and ecosystem function for both parties by enhancing the response to environmental stress and producing the same or similar compounds that originate in the host [1,2,3]. In particular, fungal endophytes have been the focus of many studies due to their prospective promise in the production of secondary metabolites with pharmacological, agricultural, industrial, or biotechnological applications [4,5,6].

Endophytic fungi were discovered over a century ago; however, it was not until about three decades ago, with the discovery of the taxol-producing endophytic fungus Taxomyces andreanae, that they gained remarkable relevance due to the abovementioned production of active secondary metabolites [7,8,9,10].

As was the case with taxol, the process for the isolation and purification of metabolites in adequate yields remains a major concern; low yields due to the exploitation of the host for the extraction process of metabolites are also associated with environmental impacts, and new strategies such as involving the use of endophytic microorganisms instead of the host themselves have offered new niches that should be meticulously investigated and used as a base for sustainable research and development [11,12].

The present review covers patents related to the production of natural products with biomedical and agricultural applications using endophytic fungi, enabling the development of new lead compounds in the process of finding new drug candidates or precursors for the synthesis of new molecules. We also cover the production of secondary metabolites in biotransformation processes by using endophytic fungi.

2. Materials and Methods

This review was conducted mainly through searches of the databases Scifinder® and Google Patents. Our search was made under the subjects “endophytic fungi” and “patents” covering the period from 2001 to 2019. 4670 references were found. After removing duplicates, we selected those related to the production of secondary metabolites and biotransformation. Resulting in 245 documents from which 224 were related to any kind of secondary metabolite derived from endophytic fungi and 21 detail biotransformation processes of metabolites through endophytic fungi. The patents covered in this study are described in Table 1 and Table 2.

Table 1

Endophytic fungi and their methods of production of natural products.

Patent No.	Endophyte	Host 1	Patent Details	Ref.
EP1142986A2	Neotyphodium sp.	Not disclosed	Chanoclavine (1)-production.	[14]
US6329193B1	Cladosporium macrocarpon	Taxus spp.	Production of taxol.	[15]
CN1421522A	Alternaria sp.	Erigeron sp.	Production of breviscapine B (2) and other flavonoids for the treatment of cardiovascular diseases and for preparing antitumor medicine.	[16]
US6638742B1	Alternaria sp.	Alnus rubra, Corylus sp., Cytisus scoparius, Ginkgo sp.	Methods for obtaining and recovering taxanes, including paclitaxel (3), from novel sources.	[17]
US6613738B1	Cryptosporiopsis cf. quercina	Tripterigeum wilfordii	Isolation of cryptocandin possessing antifungal activity.	[18]
US20040185031A1	Muscodor vitigenus	Paullinia paullinioides	Novel fungi that produces naphthalene and applications.	[19]
US20040206697A1	Muscodor albus	Cinnamon tree	Novel fungi and production of organic volatile antibiotics effective in the treatment of human and animal waste.	[20]
US20040248265A1	Phialocephala fortinii	Podophyllum sp.	Identification of podophyllotoxin-producing fungi and methods for recovering podophyllotoxin (4) from such fungi.	[21]
WO2004106487A2	Neotyphodium lolii	Pooideae grass	Production of janthitrem epoxide (5) compounds in combination with ryegrass instead of compounds that affect the health and performance of grazing animals.	[22]
CN1624103A	Mix of Taxus endophytes	Taxus chinensis	Increase the production of taxol and taxol precursors.	[23]
US6911338B2	Muscodor sp.	Cinnamomum zeylanicum, Grevillea pteridifolia	Production of organic volatile antibiotics with activity on specific plant pathogens, bacteria, nematodes and insects.	[24]
CN1850765A	Halorosellinia sp.	mangrove	Obtaining quinone compounds (6–7) with antitumor activity.	[25]
US20060134762A1	Fungal strain MTCC 5124	Mappia sp.	New source in the form of a novel endophytic fungal strain for the production of camptothecin (8) and camptothecinioids and an improved process for producing these.	[26]
US7070985B2	Muscodor albus	Cinnamomum zeylanicum	Novel fungi and production of organic volatile antibiotics effective in the treatment of human and animal waste products.	[27]
CN1896232A	Fusarium sp.	Ginkgo biloba	Production of plasmin.	[28]
CN1948459A	Cladosporium sp.	Parthenocissus tricuspidatae	Production of resveratrol (9).	[29]
CN1951907A	Aspergillus niger	Euphorbia sp.	Preparation of compound 2,3-diamino-6-hydroxy-benzoic acid-2-ethyl-hexyl ester (10), including method, and its application in pharmacy.	[30]
CN101037656A	Trichoderma harzianum	Ilex cornuta	Preparation of the sesquiterpenoids trichotec-9-en-4-ol, 12, 13, epoxy-, and 4β-acetate (11) as pesticides.	[31]
CN101041840A	Trichoderma harzianum	Ilex cornuta	Preparation of the sesquiterpenoids trichotec-9-en-4-ol, 12, 13, epoxy-, and 4β-acetate as pesticides.	[32]
US7192939B2	Pestalotiopsis microspora	Terminalia morobensis	Novel fungi strains capable of producing novel antioxidant and antimycotic agents	[33]
CN101195804A	Acremonium endophytium	Huperzia serrata	Production of huperzine A (12) analogs through strain liquid fermentation of the endophytic fungi.	[34]
CN101234951A	Aspergillus clavatonanicus	mangrove	Production of biphenyl compound (13) including preparation method and application.	[35]
CN101275116A	Mix of endophytes	Huperzia serrata	Preparation of huperzine A.	[36]
CN101240249A	Fusarium sp.	Dioscorea zingiberensis	Production of beauvericin (14) description of its antibacterial activity.	[37]
CN101280279A	Phomopsis sp.	Acer ginnala	Production of gallic acid (15).	[38]
US7341862B2	Muscodor albus	Cinnamomum zeylanicum	Novel fungi and production of organic volatile antibiotics effective in the treatment of human and animal waste products.	[39]
CN101412971A	Fusarium sp.	Paris polyphylla var. yunnanensis	Production of 5α, 8α-ergosterol peroxide-6, 22-diene-3β-ol (16), ergosterol-8(9), 22-diene-3β, 5α, 6β, 7α-tetraol (17), and succinic acid (18) as antimicrobial active ingredients.	[40]
CN101468977A	Phomopsis sp.	Azadirachta indica	Novel pseudo-phomallactone (19) antibacterial compound from fermentation products of an endophytic fungus strain.	[41]
CN101468996A	Phomopsis sp.	Azadirachta indica	Source of ten-membered lactone 7α-acetoxy-multiplolide A (20) and its applications.	[42]
CN101481379A	Chaetomium globosum	Ginkgo biloba	Obtaining chaetomugilin D (21) from an acetic acid ethyl ester extract of fermentation liquor.	[43]
CN101486974A	Aspergillus niger	Taxus cuspidata	Production of taxol from endophytic fungus.	[44]
CN101503658A	Not disclosed	Locoweed	Separation of an endophytic fungus producing swainsonine (22).	[45]
CN101525611A	Fusarium sp.	Chrysanthemum sp.	Plasmin preparation.	[46]
CN101586082A	Aspergillus candidus	Taxus x media	Production of taxol. A method for preparing taxol is also given.	[47]
US20090142816A1	Gliocadium sp.	Eucryphia cordifolia	Production of volatile compounds and hydrocarbons to generate biofuels.	[48]
CN101619291A	Chaetomium cupreum	Macleaya cordata	Preparation of 3,3′ 6,6′-tetrahydroxy-4,4′-dimethyl-1,1-bi(cyclohexa-3,6-diene)-2,2′,5,5′-tetraone (23) with antitumor properties.	[49]
CN101669939A	Not disclosed	Mangrove	Enniatin compound (24) that aids in the preparation of anti-tubercle drugs.	[50]
CN101701230A	Fusarium proliferatum	Mangrove	Improving the output of anticancer anthraquinone compound (25) by utilizing different vaccination methods.	[51]
CN101875905A	Shiraia bambusicola	Phyllostachys edulis seed	High-yield hypocrellin-producing strain that carries out hypocrellin (26) production by fermentation.	[52]
CN101914452A	Penicillium chrysogenum	Not disclosed	Huperzine A-producing strain.	[53]
KR2010104252A	Scolecobasidium tshawytschae	Soybean	Gibberellin (27) production using soybean endophyte.	[54]
WO2010062159A1	Aspergillus sp.	Garcinia scortechinii	Cyclic peptides with utility in anticancer treatments.	[55]
CN101942393A	Shiraia sp.	Huperzia serrata	Production of huperzine A.	[56]
CN102080110A	Not disclosed	Nothapodytes nimmoniana	Technical process for synthesizing a camptothecin sugar derivative.	[57]
CN102080111A	Not disclosed	Icacinaceae plant	Method for endophyte induction to produce 10-hydroxy camptothecin (28).	[58]
CN102080112A	Not disclosed	Icacinaceae plant	Method for endophyte induction to manufacture of 9-methoxycamptothecin (29).	[59]
CN102154116A	Phomopsis wenchengensis	Not disclosed	Manufacture of agricultural fungicide (30).	[60]
CN102168017A	Colletotrichum gloeosporioides	Huperzia serrata	High-producing strain and method for huperzine A production.	[61]
CN102187870A	Aspergillus oryzae	Red algae Heterosiphonia sp.	Use of diterpene alkaloid (31) secondary metabolites as pesticides.	[62]
CN102190612A	Aspergillus oryzae	Red algae	Preparation of diterpene alkaloid (32) with bacteriostatic activity that can be used for preparing antimicrobial agents.	[63]
CN102190614A	Aspergillus oryzae	Red algae Heterosiphonia sp.	Use of diterpenoid alkaloid (33) as an insecticide agent.	[64]
CN102190698A	Aspergillus oryzae	Marine algae	Preparation and application of alga endophytic fungi diterpenoid alkaloid compound (34).	[65]
CN102191294A	Acremonium endophytium	Huperzia serrata	Production of huperzine A as an anti-senile dementia pharmaceutical ingredient.	[66]
CN102190699A	Aspergillus oryzae	Marine algae	Preparation of a diterpene alkaloid-like compound (35) for use as an insecticide.	[67]
CN102220247A	Verticillium dahlia	Radix glycyrrhizae	Production of glycyrrhetic acid (36).	[68]
IN2010DE00131A	Aspergillus elegans	Asparagus racemosus	Production of antimicrobial and anticancer lactone metabolite, including an outline of the process.	[69]
JP2011051953A	Diaporthe sp.	Curcuma sp.	Manufacture of neohexa-hydro-curcumin (37).	[70]
WO2011146634A1	Hypoxylon sp./Nodulisporium sp./Daldinia sp./Muscodor sp.	Persea indica	Production of volatile organic compounds from these fungi.	[71]
CA2766412A1	Fungal endophytes of Pinus strobus	Pinus strobus	Antifungal metabolites (38–44).	[72]
CN102321545A	Penicillium steckii	Trypterigium wilfordii	Production of triptolide (45).	[73]
CN102417883A	Phomopsis sp.	Camptotheca acuminata	Production and method for preparation of camptothecin.	[74]
CN102464634A	Trichoderma atroviride	Cephalotaxus fortunei	New compound (46) in secondary metabolites of C. fortunei endophytic fungi and its preparation method and application thereof.	[75]
CN102559517A	Fusarium sp.	Podophyllum hexadrum	Preparation of podophyllotoxin.	[76]
CN102586355A	Fusarium proliferatum	Mangrove	Method for producing anticancer anthraquinone compounds.	[77]
CN102628018A	Aspergillus niger	Schisandra chinensis	Improved production of the main components schisandrol A (47), schisantherin A (48), deoxyschizandrin (49), schisandrin B (50) from S. chinensis through fermentation.	[78]
CN102633616A	Alternaria sp.	Sarcophyton sp.	Preparation of the anthraquinone dimer alterporriol P (51) as an antineoplastic agent.	[79]
CN102643167A	Aspergillus versicolor	Marine algae	Fermentation preparation and application as an antibacterial and insecticidal agent of albican-11,14-diol (52).	[80]
CN102643186A	Alternaria sp.	Sarcophyton sp.	Preparation of the anthraquinone dimers alterporriol Q (53) and alterporriol R (54) for antiviral drugs.	[81]
CN102643755A	Penicillium chrysogenum	Glycyrrhiza glabra	Endophytic fungus that improves the content of glycyrrhetinic acid by fermenting licorice.	[82]
CN102653720A	Colletotrichum gloeosporioides	Huperzia serrata	Endophytic fungus capable of generating huperzine A.	[83]
CN102660466A	Aspergillus penicillioides	Schisandra chinensis	Improves the content of the active ingredients of S. chinensis: schizandrin, schisantherin, deoxyschizandrin, and schisandrin B.	[84]
CN102660467A	Fusarium oxysporum	Glycyrrhiza glabra	Fungal strain that produces glycyrrhetinic acid.	[85]
CN102676392A	Trichoderma atroviride	Salvia miltiorrhiza	Endophytic fungus that aids in the production of tanshinone I (55) and tanshinone IIA (56).	[86]
CN102701935A	Trichoderma longibrachiatum	Seaweed	Preparation of tetranuclear diterpenoid (57) with pesticidal and bacteriostatic activity.	[87]
CN102703327A	Cladosporium sp.	Aconitum leucostomum	Fungal strain capable of synthesizing aconitine (58) for the preparation of antitumor, anti-inflammatory, and antirheumatic drugs.	[88]
CN102719362A	Alternaria sp.	Merlot grapes	Fungal strain capable of producing a large amount of resveratrol in the fermentation process.	[89]
CN102732427A	Fusarium proliferatum	Oxytropis glabra	Separation method for swainsonine-producing endophytic fungus.	[90]
CN102732428A	Fusarium oxysporum	Cajanus cajan	Endophytic fungal strain with a high yield of cajaninstilbene acid (59).	[91]
CN102787077A	Acremonium sp.	Sophora alopecuroides	Synthesis of matrine (60).	[92]
CN102807956A	Ceriporia lacerata	Cleistocalyx operculatus	Preparation of 2′,4′-dihydroxy-6′-methoxyl-3′,5′-dimethylchalcone (61).	[93]
WO2012020364A1	Fungal strain MTCC 5544	Pongamia pinnata	Dipeptide derivative (62) for the treatment of cancer.	[94]
CN103073527A	Phomopsis sp.	Illigera rhodantha	Preparation of libertellenone G (63) as a novel medicine for treating Alzheimer’s disease.	[95]
CN103074236A	Trichoderma atroviride	Camptotheca acuminata	Production and application of camptothecin.	[96]
CN103083290A	Trichoderma sp.	Not disclosed	Trichoderma acid (64) is involved in the preparation of antifungal agents.	[97]
CN103087923A	Chaetomium globosum	Ginkgo biloba	The endophytic fungus and metabolite flavipin (65) acts as an antioxidant.	[98]
CN103103134A	Colletotrichum sp.	Huperzia serrata	Production of huperzine A.	[99]
CN103194502A	Nodulisporium sylviforme	Taxus sp.	Separation and purification of taxol by biological fermentation as well as precursors such as baccatin III (66) and cephalomannine (67).	[100]
CN103288807A	Not disclosed	Trypterigium wilfordii	Separation of alkaloids (68–70) with pharmaceutical application.	[101]
CN103360351A	Xylaria sp.	Azadirachta indica	Obtaining three isopimarane diterpenoid compounds (71–73) with antifungal activity and potential applications in new agricultural or medical antifungal medicaments.	[102]
CN103436451A	Colletotrichum sp.	Cyclocarya paliurus	Production of haematochrome, including its production via a fermentation method.	[103]
IN2011DE03381A	Diaporthe sp.	Pandanus amaryllifolius	Antitubercular diaportheone B analogs (74–75) and their synthesis.	[104]
US20130137131A1	Nodulisporium sp., Daldinia sp., Hypoxylon sp.	Persea indica	System and method for producing volatile organic compounds	[105]
US20130177596A1	Colletotrichum sp.	Pteromischum sp.	Production of antifungal and immunosuppressive compounds	[106]
US20130224315A1	Muscodor strobelli	Not disclosed	Production of volatile organic compounds and methods of use	[107]
US20130252289A1	Several fungi such as Nodulisporium sp., Hypoxylon sp., Annulohypoxylon sp., Daldinia sp., Xylaria sp.	Thelypteris angustifolia, Persea indica, Citrus aurantifolia, Myroxylon balsamum, Taxodium distichum	Production of volatile organic compounds from microorganisms.	[108]
US20130302480A1	Muscodor crispans	Ananas ananassoides	Production of compounds with wide range of applications in agriculture, industrial, building, pharmaceutical and/or personal care products.	[109]
WO2013164834A1	Fusarium solani	Taxus celebica	Cost-effective process for commercial production of paclitaxel.	[110]
CN103570744A	Scopulariopsis sp.	Carijoa sp.	Preparation method for the quinazoline alkaloid compound (76) and its application as a tumor cell growth inhibitor.	[111]
CN103627736A	Fungal strain L1 CGMCC No. 4558	Polygonum cuspidatum	Extraction of resveratrol from fermented liquor.	[112]
CN103642864A	Shiraia bambusicola	Huperzia serrata	Preparation of hypocrellin compounds.	[113]
CN103667070A	Trichoderma sp.	Huperzia serrata	Preparation and application of huperzine A.	[114]
CN103667072A	Ceriporia lacerata	Huperzia serrata	Preparation of 8α, 15α-epoxy-huperzine A (77).	[115]
CN103667073A	Peyronellaea glomerata	Huperzia serrata	Preparation of pyrrole type (78) liver-protecting medicines.	[116]
CN103820331A	Ceriporia lacerata/Hypoxylon investiens	Phlegmariurus sp.	Production of huperzine A.	[117]
CN103820332A	Pycnoporus sanguineus	Huperzia serrata	Production of huperzine A.	[118]
CN103911293A	Botryosphaeria dothidea	Taxus chinensis	Strain with a high paclitaxel yield and method for producing paclitaxel.	[119]
CN103966109A	Aspergillus fumigatus	Schisandra chinensis fruit	Endophytic fungus that is capable of producing protocatechuic aldehyde (79).	[120]
CN104031948A	Daldinia eschscholzii	Gracilaria sp.	Production of dalesconol A (80) and B (81) as immunosuppressive compounds.	[121]
CN104059044A	Trichoderma sp./Penicillium sp.	Mangrove	Preparation of a xanthone derivative (82) as a microbial pesticide and fungicide.	[122]
CN104073529A	Not disclosed	Taxus x media seed	Production of taxol.	[123]
CN104086522A	Lasiodiplodia pseudotheobromae	Camptotheca acuminata	Preparation of a spiro-dinaphthalene compound (83).	[124]
CN104109691A	Not disclosed	Ginkgo biloba	Preparation and dyeing of red pigment haematochrome.	[125]
US20140082771A1	Nodulosporium spp. or Ascocoryne spp.	Lomatia fraseri or Nothofagus cunninghamii	Isolation of antibiotic compound.	[126]
CN104293678A	Cladosporium cladosporioides	Forsythia sp.	Production of forsythoside A (84), forsythoside B (85), and forsythin (86) and their applications.	[127]
CN104357525A	Acremonium dichromosporum	Glycyrrhiza sp.	Production of glycyrrhetinic acid by using microbial fermentation.	[128]
CN104450528A	Not disclosed	Gardenia jasminoides	Method for isolation and screening of endophytic fungi and for large-scale preparation of high-purity genipin (87).	[129]
CN104450531A	Fusarium tricinctum	Fritillaria cirrhosa	Obtains peiminine (88) and peimisine (89) alkaloids.	[130]
CN104593443A	Botryosphaeria rhodina	Aquilaria sinensis	Preparation of agilawood chromone (90–94) components.	[131]
CN104726345A	Mixtures of fungi including Gliocladium sp.	Taxus spp.	High production of baccatin III.	[132]
CN104762348A	Not disclosed	Gastrodia elata/Armillaria mellea	Preparation of gastrodin (95).	[133]
CN104774774A	Aspergillus fumigatus	Glycyrrhiza sp.	Production of pseutorin A (96) as a food preservative.	[134]
CN104789613A	Alternaria sp.	Spiraea salicifolia	Extraction and separation of bacteriostatic component (97) from fermentation broth.	[135]
CN104805017A	Fusarium solani	Pinellia sp.	Generation and application of β-glucosidase.	[136]
CN104877910A	Eupenicillium brefeldianum	Not disclosed	Preparation of brefeldin A (98). The compound has antifungal and insecticide activity and is an ideal veterinary and agriculture candidate drug.	[137]
CN105039173A	Mortierella sp.	Huperzia serrata	Fungal strain with a high huperzine A content.	[138]
CN105039174A	Fusarium sp.	Paeonia sp.	Production of paeonol (99).	[139]
CN105039175A	Talaromyces sp.	Paeonia sp.	Production of paeonol.	[140]
CN105039176A	Fusarium sp.	Paeonia sp.	Production of paeonol.	[141]
CN105200091A	Geomyces sp.	Nerium indicum	Production and application of ethyl vincamine (100).	[142]
US20150073048A1	Muscodor sp.	Ananas ananassoides	Production of antimicrobial composition and methods of use	[143]
WO2015029069A1	Trichoderma longibrachiatum	Boswellia serrata	Production of brachiatin D (101).	[144]
CN105238697A	Chaetomium sp.	Paeonia sp.	Production of paeonol with endophytic fungus from peony.	[145]
CN105238700A	Epicoccum nigrum	Wild soybean	High-yielding oleanolic acid endophyte.	[146]
CN105274005A	Aspergillus fumigatus	Taxus x media	Taxol production.	[147]
CN105316238A	Trichoderma sp.	Taxus chinensis	Method for culturing and screening taxol-producing fungus.	[148]
CN105349431A	Phoma glomerata	Salvia miltiorrhiza	Generation and application of salvianolic acid C (102).	[149]
CN105400842A	Fusarium mairei	Taxus x media/Valeriana jatamansi	Increases the yield of paclitaxel in an endophytic fungus fermentation product.	[150]
CN105505798A	Phoma glomerata	Salvia miltiorrhiza	Generation of ergosterol (103).	[151]
CN105506021A	Aspergillus sp.	Not disclosed	Preparation of taxol-containing culture.	[152]
CN105670940A	Mucor racemosus	Huperzia serrata	Application of a fungal strain with highly efficient expression of huperzine A.	[153]
CN105838613A	Chaetomium globosum	Cajanus cajan	Application of a fungal strain with a high yield of flavipin.	[154]
CN105925646A	Phomopsis liquidambari	Mangrove	Preparation method for cytochalasin H (104).	[155]
CN106010980A	Paraconiothyrium brasiliense	Acrida cinerea	Strain capable of producing of perlolyrine (105) and a method for preparation.	[156]
CN106047715A	Trichoderma sp.	Nothapodytes pittosporoides	Extraction of camptothecin.	[157]
WO2016034751A1	Guignardia mangiferae	Persea indica	Biocidal products (106) that are used to control phytopathogens and pest organisms.	[158]
CN106432168A	Penicillium citrinum	Bruguiera sexangula var. rhynchopetala	Preparation of isocoumarins (107–113) as antibacterial drugs.	[159]
CN106434361A	Ascomycota sp.	Mangrove	Preparation of indanone derivatives (114–115).	[160]
CN106497803A	Fusarium verticillioides	Huperzia serrata	Fungal strain with huperzine A-producing function and its use in the biosynthesis of medicine for treating Alzheimer´s disease and vascular dementia.	[161]
CN106497804A	Fusarium oxysporum	Huperzia serrata	Production of huperzine A and its application in the treatment of dementia.	[162]
CN106588944A	Neonectria sp.	Meconopsis grandis	Preparation of compound (116) derived from Tibetan medicine endophytic fungi.	[163]
CN106636247A	Not disclosed	Melia azedarach	Fermentation extraction of azadirachtin (117).	[164]
CN106701594A	Neocosmospora sp.	Meconopsis grandis	Production of pyrrocidine A (118) and pyrrocidine B (119).	[165]
CN106946955A	Pezicula sp.	Taxodium distichum	Production of mycotrisaccharide compounds (120–124) that aid in the preparation of drugs for preventing and controlling plant fungal disease.	[166]
CN106967622A	Aspergillus flavus	Torreya fargesii	Paclitaxel production.	[167]
CN106967623A	Aspergillus niger	Torreya sp.	Production of the taxane compound baccatin III.	[168]
CN106978356A	Nigrospora sphaerica	Artemisia argyi	Preparation of large amounts of bostrycin (125).	[169]
CN107034145A	Pestalotiopsis vismiae	Cordyceps sinensis	In vitro production of nucleosides, preferably, adenosine, guanylyl, uridine, and inosine.	[170]
CN107058118A	Aspergillus aculeatus	Taxus x media	Efficient taxol-producing endophytic fungus.	[171]
CN107118972A	Epicoccum nigrum	Solidago canadensis	Endophytic fungus capable of generating pectin through liquid fermentation.	[172]
CN107129936A	Penicillium sp.	Torreya fargesii	Production of paclitaxel.	[173]
CN107254504A	Fusarium sp./Bacillus aryabhattai	Erigeron breviscapus	Increasing the scutellarin (126) content with microbial agents.	[174]
CN107354182A	Purpureocillium lilacinum	Grey green soy bean	Preparation of (R)-4-benzyl-2-oxazolidinone (127) by fermentation.	[175]
WO2017049353A1	Daldinia sp.	Pittosporum bicolor	Production of volatile organic compounds as insecticidal and antifungal agents.	[176]
WO2017068223A1	Stemphylium solani	Artemisia absinthium	To obtain compounds (128–129) for use as biocides.	[177]
CN107686817A	Ascomycota sp.	Fetid marsh fleabane	Production of ascomylactam compounds (130–131).	[178]
CN107723245A	Fusarium sp.	Liriope spicata var. prolifera	Endophytic fungi and application in the steroids saponin diosgenin (132) and ruscogenin (133).	[179]
CN107723246A	Penicillium oxalicum	Liriope spicata var. prolifera	Endophytic fungi and application in the steroid saponin diosgenin and ruscogenin.	[180]
CN107723247A	Cladosporium sp.	Liriope spicata var. prolifera	Endophytic fungi and application in the steroid saponin diosgenin and ruscogenin.	[181]
CN107723248A	Penicillium sp.	Liriope spicata var. prolifera	Endophytic fungi and application in the steroid saponin diosgenin and ruscogenin.	[182]
CN107739716A	Penicillium sp.	Liriope spicata var. prolifera	Endophytic fungi and application in the steroid saponin diosgenin and ruscogenin.	[183]
CN107739717A	Schizophyllum sp.	Liriope spicata var. prolifera	Endophytic fungi and application in the steroid saponin diosgenin and ruscogenin.	[184]
CN107739718A	Aspergillus sp.	Liriope spicata var. prolifera	Application in the preparation of the steroid saponin diosgenin and ruscogenin.	[185]
CN107868757A	Bjerkandera adusta	Not disclosed	Preparation of 8α, 15α-epoxy-huperzine A, which has a curative neuroprotective effect.	[186]
CN107955793A	Aspergillus niger	Liriope spicata var. prolifera	Preparation of the steroid saponin.	[187]
CN108264473A	Penicillium decumbens	Not disclosed	Preparation and application of 1-aniline-2-pyrrolidone class compounds (134–135).	[188]
CN108277164A	Diaporthe sp.	Excoecaria agallocha	Indene derivative (136) that aids in the preparation of an anti-inflammatory drug	[189]
CN108383811A	Aspergillus tubingensis	Decaisnea fargesii	Production of furanone (137) derivative with good antibacterial activity.	[190]
CN108467398A	Trichoderma asperellum	Seaweed	Preparation of diketopiperazine compound (138), which has antibacterial application.	[191]
CN108503616A	Aspergillus tubingensis	Decaisnea fargesii	Extraction method and application of a bicoumarin derivative (139).	[192]
CN108640897A	Daldinia eschscholtzii	Mangrove	Preparation and application of polyketides (140–141).	[193]
CN108728367A	Phoma sp.	Coral gorgonian source	Preparation of antibacterial compounds (142–143).	[194]
CN108913731A	Pestalotiopsis sp.	Rhizophora stylosa	Preparation and application of pestalotiopyrone M (144) which has immunosuppressive activity.	[195]
CN109082445A	Fusarium proliferatum	Ginkgo sp.	Production and application of glycine (145), betaine (146), scopoletin (147), yagaine, rosmarinic acid (148), oxipurinol (149), resveratrol, naringenin (150), catechin (151), taxifolin (152), and xanthohumol (153), which have antibacterial properties.	[196]
CN109096056A	Aspergillus flavus	Kandelia obovata	Preparation of bisabolane sesquiterpene compounds (154-155) as anti-type II diabetes mellitus drugs.	[197]
IN201641023516A	Phomopsis sp.	Gloriosa superba	Method of producing colchicine (156) from an endophyte using epigenetic modifiers.	[198]
IN201721003140A	Phoma sp.	Litsea glutinosa	Isolation, fermentation, purification, and characterization of the antibacterial compound 2’-hydroxygenistein (157).	[199]
CN109111422A	Penicillium sp.	Panax notoginseng	Macrolide compounds (158–167) and their application in the prevention and treatment of plant-pathogenic bacteria.	[200]
CN109180635A	Xylaria curta	Solanum tuberosum	Preparation and application of compound E1011 (168).	[201]
CN109206337A	Fusarium sp.	Santalum album	Method for preparation of hexichol phenolic acid compounds (169–171) and their application in the preparation of antibacterial compounds.	[202]
CN109232481A	Not disclosed	Taxus chinensis	Preparation of high-purity taxol.	[203]
CN109234175A	Fusarium oxysporum	Paris polyphylla	Production of chonglou saponin (172–175).	[204]
CN109265397A	Lophiostoma sp.	Eucalyptus exserta	Fast separating process of fungal secondary metabolites (176–177).	[205]
CN109293494A	Talaromyces sp.	Mangrove	Method for preparation of 1, 4-naphtoquinone compounds (178–179) and their application in the preparation of anti-inflammatory drugs.	[206]
CN109439705A	Aspergillus sp.	Soft coral	Microbe preparation of subergorgic acid (180).	[207]
CN109456191A	Cerrena sp.	Pogostemon cablin	Preparation of cerrenin D (181) that is applied in the preparation of antitumor drugs.	[208]
CN109456899A	Penicillium notatum	Gastrodia elata	Fermentation and production of penicillic acid (182).	[209]
CN109486685A	Penicillium sp.	Mangrove	Preparation of anti-insect activity terpenes (183–184) as crystalline compounds.	[210]
CN109503414A	Trichoderma asperellum	Seaweed	Preparation of one kind of alkane sesquiterpene derivative (185).	[211]
CN109503428A	Trichoderma asperellum	Seaweed	Preparation of a cyclonerolane-type hydroxamic acid derivative (186).	[212]
CN109503535A	Trichoderma asperellum	Seaweed	Preparation of a bicyclic cyclonerolane type sesquiterpene derivative (187).	[213]
CN109503623A	Trichoderma koningiopsis	Morinda officinalis	Preparation and application of guanacaste class compounds (188–189) in the preparation of antibacterial compounds.	[214]
CN109553600A	Penicillium sp.	Mangrove	Preparation and application of isocoumarin class compounds (190–197).	[215]
CN109651125A	Fungal strain ZJY1288 GDMCC No. 60290	Mangrove	Preparation and application of anthraquinone metabolites (198–199)	[216]
CN109776561A	Cytospora rhizophorae	Morinda officinalis	Preparation of cytorhizin B (200) and C (201) that are applied in the preparation of antitumor drugs.	[217]
CN109810906A	Bionectria pityrodes	Tamarix sp.	Preparation of phenolic acid compound (202) through fermentation.	[218]
CN109956883A	Trichoderma asperellum	Seaweed	Preparation of an azo-cyclo alkane type sesquiterpene derivative (203) produced through an acetylation method.	[219]
CN109971652A	Onygenales sp.	Incarvillea younghusbandii	Preparation of gymnoascolide A (204) in preparing anti-inflammatory drugs.	[220]
CN109971651A	Arthrinium arundinis	Tobacco	Preparation of 5, 8-peroxyde of ergosterol.	[221]
CN109971655A	Chaetomium sp.	Radix astragali	Production of differanisole A (205).	[222]
CN109988181A	Bipolaris sp.	Lycium barbarum	Preparation of bipolahydroquinone C (206) that is used as an antineoplastic drug for treating human pulmonary squamous carcinoma and breast carcinoma.	[223]
CN110093383A	Alternaria sp.	Polygonum senegalense	Preparation of compound alterlactone (207) that is used as a disinfectant in agriculture.	[224]
CN110218200A	Pseudopithomyces sp.	Sonneratia caseolaris	Preparation of depsipeptide compound (208).	[225]
CN110229127A	fungal strain TGM112 CGMCC No. 16499	Mangrove	Preparation of butyrolactone compounds (209–211).	[226]
CN110257255A	Daldinia eschscholtzii	Mangrove	Preparation of chromone derivatives (212–216).	[227]
CN110257260A	Boeremia exigua	Atractylodis macrocephalae	Preparation of the Atractylodes lactones I (217) and II (218).	[228]
CN110272828A	Colletotrichum boninense	Huperzia serrata	New microbe resource for the production of huperzine A industrial fermentation.	[229]
CN110283728A	Daldinia eschscholtzii	Mangrove	Preparation of tetralone derivatives (219–223).	[230]
CN110295116A	Aspergillus sp.	Tamarix sp.	Production of a variety of fatty acids and their application.	[231]
CN110302215A	Penicillium sp.	Taxus x media	Fungal crude extract, it‘s applications, e.g., as being a source of paclitaxel analog.	[232]
CN110438015A	Aspergillus tamarii	Citron orange fruit	Fungal strain its fermentation to produce hesperidinase.	[233]
CN110484588A	Acremonium pilosum	Mahonia sp.	Preparation of fusidic acid (224).	[234]
CN110511876A	Ilyonectria cyclaminicola	Korean Epimedium herb	The culture method of this fungal strain and its metabolites epimedins A–C (225–227).	[235]
CN110563740A	Aspergillus fumigatus/Fusarium oxysporum	Edgeworthia chrysantha/Stachys japonica	Methods for preparation and application of alpha-pyrone (228).	[236]
IN201721002537A	Aspergillus japonicus	Achryranthes aspera	Production of the novel antibacterial compound fraxidin (229).	[237]

1 Some patents just provided a common name for the host organism.

Table 2

Endophytic fungi applied for biotransformation.

Patent No.	Endophyte	Host 1	Patent Details	Ref.
CN102080048A	Absidia glauca	gingsen	Conversion of ginsenoside Rb1 (230) to prepare ginsenoside Rd (231).	[245]
CN102080049A	Zygorhynchus moelleri	Panax gingsen	Preparation of ginsenoside Rd from ginsenoside Rb1.	[246]
CN102154123A	Fusarium sp.	Dioscorea nipponica	Biotransformation conversion conditions of diosgenin saponins.	[247]
CN102199548A	Penicillium oxalicum	Polygonun cuspidatum	Microbial transformation of resveratrol from polydatin (232).	[248]
CN102212486A	Penicillium oxalicum	Polygonun cuspidatum	Conversion of polydatin into resveratrol.	[249]
CN102392050A	Penicillium sp.	Not disclosed	Biotransformation of raisin extract. Preparation and application in flavoring.	[250]
CN102757443A	Several endophytes featuring Penicillium purpurogenum	Dysosma sp. or Sabina vulgaris	Separation and purification method for bioconversion of podophyllotoxin into sulfur-substituted derivatives.	[251]
CN103695478A	fungal strain L1 CGMCC No. 4558	Not disclosed	Conversion of polydatin to resveratrol.	[252]
CN103981104A	Microsphaeropsis arundinis	wild rice	Biotransformation of glycyrrhizinic acid (233) into liquiritin (234).	[253]
CN103992953A	Aspergillus flavus	wild rice	Transform glycyrrhizic acid into glycyrrhetinic acid monoglucuronide (235).	[254]
CN106591142A	Xylariales sp.	Not disclosed	Conversion of Panax notoginseng saponin to prepare vina-ginsenoside R13 (236), notoginsenoside J (237) and American saponin ginseng L16 (238).	[255]
CN106701604A	Chaetomium globosum	wild rice	Conversion of glycyrrhizic acid into glycyrrhetinic acid monoglucuronide.	[256]
CN106893677A	Fusarium sp.	Herba Andrographitis	Transformation of andrographolide diterpenoids (239–242).	[257]
CN107034253A	Fusarium oxysporum	Gentiana sp.	Conversion of gentiopicroside (243) into two separate compounds with hepatoprotective activity.	[258]
CN107312720A	Fusarium proliferatum	Cajanus cajan	Conversion of ginsenoside Rb1 into ginsenoside Rd and its application.	[259]
CN108707553A	Plectosphaerella cucumerina	Huperzia serrata	Efficient conversion of androstenedione to testolactone and androstane diene diketone.	[260]
CN109536561A	Fusarium oxysporum	gingsen	Conversion of ginsenoside Rb1 into the rare ginsenoside CK (244).	[261]
CN110527632A	Phomopsis sp.	Not disclosed	Bioconversion of betulinic acid (245).	[262]
CN110423697A	Lasiodiplodia pseudotheobromae	Illicium verum	trans-trans-Anethole (246) conversion to generate different vanillic acids (247).	[263]
US20190264295A1	Ovatospora brasiliensis	Curcuma sp.	Microbial bioconversion of curcuminoids to calebin A (248).	[264]
WO2019070219A2	Alternaria eureka/Neosartorya hiratsukae/Camarosporium laburnicola	Astragalus condensatus, A. angustifolius	Production of a telomerase activator, biotransformation with endophytic fungi to obtain new/novel molecules from the saponins from natural sources and method for discovery molecules that increase telomerase enzyme activation.	[265]

1 Some patents just provided a common name for the host organism.

3. Results

The description and analysis of patents was divided into two sections: those that are connected to the production of secondary metabolites and those associated with biotransformation processes. Likewise, two tables were constructed in which the main generalities of each patent are summarized.

3.1. Production of Secondary Metabolites

Early patents consisted mainly of registering the endophytic strains capable of producing specific compounds or those that represented a novel source of active metabolites (chanoclavine in EP1142986A2; resveratrol in CN1948459A; gallic acid in CN101280279A; taxol in CN101486974A) and very few applications. However, over time, patents were developed to include the registration of methods and procedures to produce and recover the compounds of interest (with a known biomedical application) or to optimize or increase their production (podophyllotoxin in US20040248265A1; taxol in CN1624103A; camptothecin in US20060134762A1; huperzine A in CN101275116A). In the last ten years, patents have been focused on using novel or enhanced fermentation processes to obtain high yields of products and provide possible applications for the metabolites (alpha-pyrone in CN110563740A; epimedins A–C in CN110511876A; differanisole A in CN109971655A; 5, 8-ergosterol epoxide in CN109971651A). The distribution of the patents in relation with the principal areas of application are illustrated in Figure 1. The production of taxol and huperzine A were considered as other application outside of their anticancer and anti-Alzheimer property respectively, due to the number of patents and economic importance.

Figure 1

Progression on the patents and fields of application in the periods 2001–2009 compared to 2010–2019. x-axis year; y-axis numbers of patents.

The principal applications consist on providing metabolites that are precursors of bioactive molecules (baccatin III and cephalomannine in CN103194502A) and those that can be use as anticancer, antitumor, antineoplastic or immunosuppressive agents (anthraquinone compounds in CN102586355A; cerrenin D in CN109456191A; alterporriol P in CN102633616A; dalesconol A and B in CN104031948A; quinazoline alkaloid compound in CN103570744A); in pesticides, insecticidal, algal control (diterpene alkaloid-like compounds in CN102190699A); as antibacterial, antibiotic, antimicrobial, bacteriostatic (beauvericin in CN101240249A; diterpene alkaloid compound in CN102190612A); as antifungal and antimycotics (Trichoderma acid in CN103083290A); in neurodegenerative diseases and neuroprotective agent (huperzine A in CN102191294A); as agents in pharmacy, food, cosmetics, agriculture and health care products (pseutorin A in CN104774774A; alterlactone in CN110093383A); antioxidant (flavipin in CN103087923A); anti-inflammatory and anti-rrheumatic (1,4-napthoquinones in CN109293494A); in cardiovascular diseases (breviscapine in CN1421522A); anti-diabetes (2 isabolene sesquiterpenes in CN109096056A); anti-tuberculosis (enniatin compounds in CN101669939A); antiviral (alterporriol Q and R in CN102643186A); as pigments; hepatoprotective agents (pyrrole-type compounds in CN103667073A); in biofuels. Table 1 displays the patents, endophytic fungi, host organism, secondary metabolites, and disclosed applications. The structures of the compounds listed in Table 1 and Table 2 are shown in Figure S1 (see the Supplementary Information).

The principal endophytic fungi reported in this section of patents belong to the genera Aspergillus, Fusarium, Trichoderma, Penicillium, and Phomopsis with 31, 24, 18, 16, and 8 patents, respectively, and compounds such as taxol or paclitaxel, huperzine A, camptothecin, podophyllotoxin, and resveratrol. Methods for enhancing their production represented most of the registered applications. Furthermore, the diversity of compound structures demonstrates the capability of fungi to synthetize simple or very complex molecules.

Mostly, Aspergillus endophytes from plants of the genera Taxus and Torreya are described as having applications related to obtaining the highest yield of paclitaxel or its precursors, like baccatin III and cephalomannine, due to their anticancer activity. Endophytes from Huperzia serrata have been linked to the production of huperzine A and its analogs due to their anti-senile dementia and anti-neurodegenerative applications. Plant endophytes such as Nothapodytes nimmoniana and Camptotheca acuminata have been linked to the production of the antineoplastic agent camptothecin and some analogs. Production of the lignan-type compound podophyllotoxin has been described for several endophytes. This compound has high biomedical potential as an anticancer, antiviral, and antibacterial agent, among others, and is the precursor of the anticancer drugs etoposide and teniposide. The stilbenoid compound found on grape skin, resveratrol, could have promising therapeutic actions against obesity, type II diabetes mellitus, metabolic syndrome, cancer, autism, dementia, and Alzheimer’s disease [13]. Therefore, a number of patents involving endophytes of the genera Cladosporium, Fusarium, Alternaria, and Penicillium for its production were registered. The demand for natural resveratrol has gained traction in various end-use industries.

3.2. Biotransformation by Endophytic Fungi

Biotechnological processes enable the production of useful molecules with a decrease in the generation of pollutants, reducing the use of solvents and reagents, minimizing the consumption of energy, and providing a way to obtain active compounds with greater specificity and efficiency. The use of endophytic fungi in biotechnological processes, such as biotransformation, is in its early stages of development and has some limitations [238]. However, there have been some reports of fungi that have been used in biotransformation [239,240,241,242].

Table 2 lists a group of patents that illustrate the efforts toward using endophytic fungi to obtain molecules of biological importance such as the ginsenosides [243] and glycyrrhetinic acid monoglucuronide [244].

Fungi from the genera Absidia, Zygorhynchus, Xylaria, and Fusarium have been patented to obtain ginsenoside Rd by the transformation of ginsenoside Rb1. Fungi from the genera Microsphaeropsis, Aspergillus, and Chaetomium have been patented for the biotransformation of glycyrrhizinic acid into glycyrrhetinic acid monoglucuronide.

4. Discussion

The study of endophytic fungi as a source of bioactive secondary metabolites has its first beginnings in 1993 with the discovery of taxol [4], until then, the primary sources of active natural molecules were isolated mainly from plants [266]. About two decades ago, the study of endophytic fungi as producers of active molecules has been emphasized due to obtaining compounds originally produced by plants or due to the production of novel secondary metabolites [11,267], Thus, fungi from genus Aspergillus, Fusarium, Penicillium and Pestalotiopsis has been recognized as producers of anticancer compounds and having pharmaceutical potential [12,268]. It is estimated that only around 1% of the microorganisms have been cultivated, and within this groups, endophytic fungi corresponded to the least studied [269].

Through this review, we have demonstrated the wide number of endophytic fungi involved in the development of methods and techniques for the application of isolation and fermentation to obtain secondary metabolites with high potential and applications in biomedicine, agriculture, and biotechnology processes. Figure 2 shows the number of patents registered for secondary metabolites and biotransformation processes through endophytic fungi for the period from 2001 to 2019. We found 224 patents related to secondary metabolites and 21 patents related to biotransformation. Aspergillus, Fusarium, Trichoderma, Penicillium, and Phomopsis were the most representative genera for secondary metabolites.

Figure 2

Number of registered patents from 2001 to 2019 linked to endophytic secondary metabolites and biotransformation processes through endophytic fungi.

Fusarium and Penicillium were the most commonly registered endophytic fungi genera among the 21 patents reviewed for biotransformation processes. Figure 3 shows the number of patented genera. The most notable applications patented were antimicrobial, antibacterial, anticancer, and those related to neurodegenerative diseases. For biotransformation processes, the conversion of ginsenosides and glycyrrhizinic acid were the most patentable applications due to their importance and potential in the pharmaceutical and food industries.

Figure 3

Number of patents reported for various endophytic fungi by genera.

Table 1 and Table 2 showed that the majority of the endophytic fungi were derived from plants, but we could also find patents where the host was soft corals or insects.

The global market for compounds like taxol is expected to reach USD $99 million by 2021 [270], and for resveratrol, the projected growth from 2018 to 2028 in revenue terms is 8.1% from USD $97.7 million [271]. Under the objectives of the 1992 Convention on Biological Diversity for the sustainable use of its components and the Nagoya Protocol on Access to Genetic Resources and the Fair and Equative sharing of benefits derived from the use of genetic resources [272], endophytic fungi and their derived compounds could open a new set of industries and economics in development countries with high biodiversity for the low-cost yield of high-profit molecules that can be applied in the fields discussed in this review.