CN116925081A - Cyclic peptide compound and application thereof - Google Patents

Cyclic peptide compound and application thereof Download PDF

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Publication number
CN116925081A
CN116925081A CN202210377247.XA CN202210377247A CN116925081A CN 116925081 A CN116925081 A CN 116925081A CN 202210377247 A CN202210377247 A CN 202210377247A CN 116925081 A CN116925081 A CN 116925081A
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group
compound
substituted
unsubstituted
alkyl
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杨财广
张涛
王蓬宇
魏柄妍
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Shanghai Institute of Materia Medica of CAS
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Shanghai Institute of Materia Medica of CAS
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Priority to CN202210377247.XA priority Critical patent/CN116925081A/en
Priority to PCT/CN2023/087687 priority patent/WO2023198076A1/en
Publication of CN116925081A publication Critical patent/CN116925081A/en
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/496—Non-condensed piperazines containing further heterocyclic rings, e.g. rifampin, thiothixene
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/4985—Pyrazines or piperazines ortho- or peri-condensed with heterocyclic ring systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/4995—Pyrazines or piperazines forming part of bridged ring systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/53—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with three nitrogens as the only ring hetero atoms, e.g. chlorazanil, melamine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A61K31/5377—1,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
    • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
    • C07D471/08—Bridged systems
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D487/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains two hetero rings
    • C07D487/04—Ortho-condensed systems

Abstract

The application provides a ClpP regulator and application thereof. Specifically, the application provides a cyclopeptide compound shown in the following formula I and a composition containing the cyclopeptide compound. The compounds can be used for preparing pharmaceutical compositions for preventing and/or treating diseases or symptoms related to ClpP protease activity or expression level.

Description

Cyclic peptide compound and application thereof
Technical Field
The application relates to the field of pharmaceutical chemistry, in particular to a cyclopeptide compound or pharmaceutically acceptable salt or stereoisomer thereof and application thereof.
Background
The ClpP gene was first found in e.coli and is highly conserved in almost all species. The ClpP protease is an important component of the Clp hydrolysis system and is an ATP-dependent proteolytic enzyme comprising a serine protease catalytic triplet domain. Typically with AAA + The molecular chaperones ClpX of the family are combined to form a ClpXP protease complex, abnormal or misfolded protein substrates in bacteria can be unfolded, and then substrate molecules are transferred to a hydrolysis cavity of the ClpP protease for degradation, so that the stability and activity of the functions of the proteins in bacteria are regulated, and the various biological functions of the bacteria are influenced. The small molecule can effectively inhibit the growth of bacteria by regulating the function of ClpP. Furthermore, studies have shown that activation and inhibition of mitochondrial ClpP function is associated with multiple functions in an organism.
Inhibitors of ClpP. The inhibitor of ClpP can occupy the binding pocket of ClpP with chaperone protein ClpX, thereby inhibiting ClpXP from exerting normal biological functions. Studies have shown that small molecule inhibitors of ClpP can affect the formation of bacterial biofilms, altering the sensitivity of bacteria to temperature and oxygen content. Inhibition of ClpP function in mitochondria can effectively kill acute myeloid leukemia cells without affecting normal cells.
An agonist of ClpP. The ClpP small molecule agonist can trigger the remodelling of the structure of the ClpP protease complex, rearrange the core structure of the ClpP protease, lead the protein to deviate from the regulation of a normal mechanism and greatly degrade certain functional proteins in cells. Studies have shown that small molecule agonists of ClpP can inhibit bacterial growth.
Thus, there is an urgent need in the art to develop novel small molecule modulators with ClpP inhibitory or/and ClpP activating effects.
Disclosure of Invention
It is an object of the present application to provide novel small molecule modulators of ClpP.
In a first aspect of the present application there is provided a cyclic peptide compound of formula I, or a pharmaceutically acceptable salt or stereoisomer thereof:
wherein Y is selected from the group consisting of: n or CR 8 ；
s is 1 or 2;
X 1 、X 2 each independently selected from the group consisting of: o, S, CH 2 Or NH;
l is selected from the group consisting of: H. substituted or unsubstituted C 1 -C 10 Alkyl, -C (O) -A-, -C (O) - (CH) 2 ) p -C(O)-A-、-C(O)NH-A-、-C(O)NH-(CH 2 ) p -C(O)-A-、-C(O)NH-(CH 2 ) p -C(O)O-A-、-S(O) 0-2 -A-, -NHC (O) NH-A-, -C (S) NH-A-, -NHC (S) NH-A-, -C (NH) NH-A-, -NHC (NH) NH-A-; p is selected from the group consisting of: 0.1, 2,3, 4 or 5;
R 1 selected from the group consisting of: H. halogen, unsubstituted C1-C10 alkyl, C1-C4 alkyl substituted with one or more Ra groups (1, 2,3, 4, 5 or more), C1-C4 haloalkyl, C2-C6 alkenyl, C2-C6 alkynyl, C1-C6 alkoxy, C1-C6 alkylthio, -NRbRc, C3-C8 cycloalkyl, C3-C8 heterocyclyl, unsubstituted C6-C10 aryl, C5-C8 heteroaryl, or C6-C10 aryl substituted with one or more Ra groups (1, 2,3, 4, 5 or more); wherein the Ra group is selected from the group consisting of: halogen, C1-C4 haloalkyl (preferably fluoro), C1-C4 alkyl, C1-C4 alkoxy, cyano, amino, or two adjacent Ra groups taken together with the atoms to which they are attached form a C5-C7 carbocyclic or heterocyclic ring; rb, rc are each independently C1-C4 alkyl, or Rb, rc together with the atom to which they are attached form a C5-C7 carbocyclic or heterocyclic ring; and when L is-C (O) NH-CH 2 -when R 1 Is not unsubstituted phenyl;
a is selected from unsubstituted C1-C8 alkylene, C1-C4 alkylene substituted with one or more Rd groups, or C1-C8 alkenylene (including monoalkenylene and dienylene); and when L is-C (O) -A-, the Rd group is selected from amino or-NHBoc;
R 2 is a group selected from the group consisting of:
or n-octyl, n-butyl;
wherein R is 7 Selected from the group consisting of: H. CH (CH) 3 、F、Cl、Br、I、OH、SH、NH 2 、CN、CF 3 、OCH 3 、SCH 3 、NHCH 3 、N(CH 3 ) 2 、CHF 2 、OC 2 H 5 、COOH、CONH 2 ；
n=0, 1,2,3, 4, 5, 6, 7, 8, 9, 10; q is selected from the group consisting of: 0.1, 2,3, 4 or 5;
R 3 、R 3 ' each independently selected from the group consisting of: H. halogen, substituted or unsubstituted C1-C4 alkyl, substituted or unsubstituted C2-C6 alkenyl, substituted or unsubstituted C2-C6 alkynyl; or R is 3 And R is 3 ' and the carbon atoms to which they are attached together form a substituted or unsubstituted saturated, partially unsaturated or aromatic 5-8 membered carbocyclic or heterocyclic ring;
R 8 is H or C1-C4 alkyl, or R 8 And R is R 3 Together forming a C1-C4 alkylene group;
R 4 is thatWherein ring a and ring B are each independently substituted or unsubstituted saturated, partially unsaturated, and/or aromatic 5-14 membered carbocycle or heterocycle (including monocyclic, fused or spiro), and ring a and ring B are fused to form a polycyclic fused ring; wherein R is 4 Optionally substituted by Re selected from halogen, C1-C4 alkyl, C1-C4 alkoxy;
R 5 selected from H, C1-C3 alkyl;
when each CH is 2 And NH, alone or as part of another group, may be optionally substituted;
unless specifically stated otherwise, the term "substituted" means that one or more hydrogen atoms on the group are replaced with a substituent selected from the group consisting of: halogen, oxo, carboxyl, cyano, hydroxyl, phenyl, 5-6 membered heterocyclyl, C1-C6 alkyl, C1-C6 alkoxy, C3-C8 cycloalkyl substitution, amino, N-dimethylamino, mercapto, C 1 -C 6 And (3) sulfonyl.
In another preferred embodiment, the compound has the structure shown in formula II:
wherein X is 3 Selected from O or S;
X 1 、X 2 、R 1 、R 2 、R 3 、R 3 ’、R 4 、R 5 the Y, A are as described above.
In another preferred embodiment, X 3 Is O.
In another preferred embodiment, Y is N.
In another preferred embodiment, X 1 、X 2 Each independently is O.
In another preferred embodiment, R 3 、R 3 ' are each independently H or C1-C4 alkyl, preferably H.
In another preferred embodiment, R 1 Selected from H, halogen, unsubstituted C1-C10 alkyl, C1-C4 haloalkyl, C3-C8 cycloalkyl, C3-C8 heterocyclyl, unsubstituted C6-C10 aryl, or C6-C10 aryl substituted with one or more Ra groups (1, 2,3, 4, 5, or more).
In another preferred embodiment, the Ra group is selected from the group consisting of: halogen, C1-C4 haloalkyl (preferably fluoro), C1-C4 alkyl, C1-C4 alkoxy, cyano, amino, or two adjacent Ra groups taken together with the atoms to which they are attached form 5-a 7 membered carbocycle or heterocycle; and when L is-C (O) NH-CH 2 -when R 1 Not unsubstituted phenyl.
In another preferred embodiment, when L is-C (O) NH-A-, R 1 Not unsubstituted phenyl.
In another preferred embodiment, R 1 Selected from H, halogen, C1-C4 haloalkyl, C3-C8 cycloalkyl.
In another preferred embodiment, the haloalkyl is preferably fluoroalkyl or chloroalkyl.
In another preferred embodiment A is C1-C8 alkylene, preferably C1-C4 alkylene, more preferably- (CH) 2 ) 1-4 -。
In another preferred embodiment, R 2 Is a group selected from the group consisting of:
n=0, 1,2,3, 4, 5, 6, 7, 8, 9, 10; q is selected from the group consisting of: 0.1, 2,3, 4 or 5;
in another preferred embodiment, R 7 Selected from the group consisting of: H. CH (CH) 3 、F、Cl、Br、I、OH、SH、NH 2 、CN、CF 3 、OCH 3 、SCH 3 。
In another preferred embodiment, when L is-C (O) NH-A-, R 2 Not be of
In another preferred embodiment, n=0 or 1.
In another preferred embodiment, R 2 Is a group selected from the group consisting of:
n＝0、1、2、3、4、5、6、7、8、9、10。
in another preferred embodiment, R 4 Is thatWherein ring a and ring B are each independently a substituted or unsubstituted aromatic 5-14 membered carbocyclic or heterocyclic ring (including monocyclic, fused or spiro ring), and ring a and ring B are fused to form a bicyclic fused or tricyclic fused ring.
In another preferred embodiment, the compound of formula I is selected from the group consisting of:
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in another preferred embodiment, the compound further comprises a compound selected from the group consisting of:
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in a second aspect of the application, there is provided a pharmaceutical composition comprising the following components:
1) A therapeutically effective amount of one or more compounds of the first aspect of the application, or a pharmaceutically acceptable salt or stereoisomer thereof;
2) A pharmaceutically acceptable carrier or excipient; and
3) Optionally a second therapeutic agent, said second therapeutic agent being an antibacterial agent.
In another preferred embodiment, the second therapeutic agent is selected from the group consisting of: ciprofloxacin, rifampin, linezolid, or a combination thereof.
In a third aspect of the application there is provided the use of a compound according to the first aspect of the application, or a pharmaceutically acceptable salt or stereoisomer thereof, for the preparation of a pharmaceutical composition for the prophylaxis and/or treatment of a disease or condition associated with ClpP protease activity or expression level.
In another preferred embodiment. The disease or disorder related to the activity or expression amount of ClpP protease is a disease or disorder caused by infection.
In another preferred embodiment, the disease or disorder associated with ClpP protease activity or expression level is cancer.
In another preferred embodiment, the infection is a bacterial infection.
In another preferred embodiment, the bacterial infection is a gram positive bacterial infection.
In another preferred embodiment, the bacterium is a gram positive bacterium: preferably, the bacteria are selected from the group consisting of: staphylococci, methicillin-resistant Lin Putao cocci, penicillin-resistant streptococcus pneumoniae, vancomycin-resistant staphylococcus aureus, streptococcus pneumoniae, enterococcus faecalis, streptococcus pyogenes.
In another preferred embodiment, the infection may be caused by one or more of the bacteria simultaneously.
In another preferred embodiment, the treatment comprises the use of the pharmaceutical composition alone or in combination with a conventional antibacterial agent.
In another preferred embodiment, the cancer is selected from the group consisting of: glioma, solid tumor, leukemia, or a combination thereof.
In another preferred embodiment, the solid tumor is selected from the group consisting of: renal cancer, liver cancer, prostate cancer, melanoma, colon cancer, lung cancer, pancreatic cancer, ovarian cancer, breast cancer, gastric cancer, brain cancer, rectal cancer, melanoma, ovarian cancer, or a combination thereof.
In another preferred embodiment, the glioma is selected from the group consisting of: glioma, brain glioma, astrocytoma, or a combination thereof.
It is understood that within the scope of the present application, the above-described technical features of the present application and technical features specifically described below (e.g., in the examples) may be combined with each other to constitute new or preferred technical solutions. And are limited to a space, and are not described in detail herein.
Drawings
FIG. 1 shows the results of the test of biological test example 3 for compounds A28, B29 in combination with rifampin and ciprofloxacin.
Detailed Description
The inventor based on molecular recognition mechanism of small molecules and ClpP proteins, rationally designed and studied in depth, found a class of ClpP regulator which is completely different from the existing ClpP regulating small molecule structure and has excellent regulating effect. The cyclic peptide compound can be used as a regulator of ClpP protease to treat pathogenic bacteria infection, such as staphylococcus, methicillin-resistant staphylococcus infection and the like, so that the cyclic peptide compound is applied to prevention and treatment of bacterial infection diseases. The present application has been completed on the basis of this finding.
Definition of the definition
As used herein, the term "alkyl" includes straight or branched chain alkyl groups. For example, C1-C6 alkyl represents a straight or branched alkyl group having 1 to 6 carbon atoms, such as methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tert-butyl, etc.
As used herein, the term "alkylene" refers to a linear or branched alkane having two bonds substituted, e.g., C1-C4 alkylene represents a linear or branched C1-C4 alkane having two bonds substituted, e.g., methylene, ethylene, n-propylene, isopropylene, butylene, and the like.
As used herein, the term "alkenyl" includes straight or branched alkenyl groups. For example, C2-C6 alkenyl refers to straight or branched alkenyl groups having 2 to 6 carbon atoms, such as vinyl, allyl, 1-propenyl, isopropenyl, 1-butenyl, 2-butenyl, or the like.
As used herein, the term "alkenylene" refers to a straight or branched chain olefin having two bonds substituted. Wherein the olefins may include mono-olefins and diolefins, such as conjugated diolefins. For example, C2-C6 alkenylene means a linear or branched C2-C6 olefin in which two bonds are substituted, such as vinylidene, n-propenyl, isopropenyl, butenylene, 1, 3-butadienylene, and the like.
As used herein, the term "alkynyl" includes straight or branched chain alkynyl groups. For example, a C2-C6 alkynyl refers to a straight or branched chain alkynyl group having 2 to 6 carbon atoms, such as ethynyl, propynyl, butynyl, or the like.
As used herein, the term "C1-C6 alkoxy" refers to a straight or branched chain alkoxy group having 1 to 6 carbon atoms; for example, methoxy, ethoxy, propoxy, isopropoxy, butoxy, isobutoxy, tert-butoxy and the like.
As used herein, the term "C1-C6 alkylthio" refers to-S- (straight or branched alkyl having 1 to 6 carbon atoms); for example, methylthio, ethylthio, propylthio, isopropylthio, butylthio, isobutylthio, t-butylthio and the like.
As used herein, the term "C3-C8 cycloalkyl" refers to cycloalkyl groups having 3-8 carbon atoms. It may be a single ring, such as cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or the like. But also in the form of a bicyclic ring, for example a bridged or spiro ring.
As used herein, the term "C3-C8 heterocyclyl" refers to a saturated or partially saturated cyclic group having 3 to 8 atoms and wherein 1 to 3 atoms are heteroatoms selected from N, S and O. It may be a single ring or may be in the form of a double ring, for example in the form of a bridged or spiro ring. Specific examples may be oxetane, azetidine, tetrahydro-2H-pyranyl, piperidinyl, tetrahydrofuranyl, morpholinyl, pyrrolidinyl and the like.
As used herein, the term "C6-C10 aryl" refers to an aryl group having 6 to 10 carbon atoms, for example, phenyl or naphthyl and the like.
As used herein, the term "C5-C8 heteroaryl" refers to a cyclic aromatic group having 5 to 8 atoms and wherein 1 to 3 atoms are heteroatoms selected from N, S and O. It may be a single ring or may be in the form of a fused ring. Specific examples may be pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, pyrrolyl, pyrazolyl, imidazolyl, (1, 2, 3) -triazolyl, and (1, 2, 4) -triazolyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, and the like.
Unless otherwise indicated as "substituted or unsubstituted", the radicals according to the application may be substituted by substituents selected from the group consisting of: halogen, nitrile, nitro, hydroxy, amino, C1-C6 alkyl-amino, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C1-C6 alkoxy, haloC 1-C6 alkyl, haloC 2-C6 alkenyl, haloC 2-C6 alkynyl, haloC 1-C6 alkoxy, allyl, benzyl, C6-C12 aryl, C1-C6 alkoxy-C1-C6 alkyl, C1-C6 alkoxy-carbonyl, phenoxycarbonyl, C2-C6 alkynyl-carbonyl, C2-C6 alkenyl-carbonyl, C3-C6 cycloalkyl-carbonyl, C1-C6 alkyl-sulfonyl, and the like.
As used herein, "halogen" refers to F, cl, br, and I.
As used herein, the term "haloalkyl" refers to a C1-C3 alkyl group substituted with a halogen. Preferably, the haloalkyl is trifluoromethyl, difluoromethyl, trifluoromethoxy. Here, "C1-C3 alkyl" means a straight-chain or branched alkyl group having 1 to 3 carbon atoms, such as methyl, ethyl, n-propyl, isopropyl.
Unless otherwise specified, the structural formulae described herein are intended to include all isomeric forms (e.g., enantiomers, diastereomers and geometric isomers (or conformational isomers)): for example R, S configuration containing asymmetric centers, the (Z), (E) isomers of double bonds, etc. Thus, individual stereochemical isomers of the compounds of the application or mixtures of enantiomers, diastereomers or geometric isomers (or conformational isomers) thereof are all within the scope of the application.
As used herein, the term "enantiomer" refers to an isomer of a compound having the same formula, which enantiomers are mirror images of each other due to the different spatial arrangement of atoms. For example, R, S configuration with asymmetric centers.
Compounds as modulators of ClpP
Design principle of the compound: the active ingredient structure of the application is designed by a recognition mechanism based on a complex crystal structure of small molecules and ClpP, namely: the small molecule regulator consists of a rigid framework and two parts of side arms, and the small molecule is respectively combined with two hydrophobic pockets of ClpP protein under the supporting action of the rigid framework to regulate the activity of ClpP and influence various biological functions. The partial rigid skeleton structure is different from the skeleton of the ClpP related regulator reported in the prior literature, and the application further obtains the small molecular compound with different regulating activities on the ClpP protein through optimizing the skeleton structure and the side arm structure.
The compounds related to the application are designed based on molecular recognition action mechanisms of small molecules and ClpP proteins, and the structural design sources are reasonable.
As used herein, "compounds of the application" refers to compounds of formula I and other compounds listed in the present application that have the effect of modulating ClpP, and also includes and various pharmaceutically acceptable salts or stereoisomers of the above compounds.
Preferred compounds of the application include compounds (including stereoisomers of each class of R and/or S configuration, and/or cis-trans isomers of E-/Z-), of each compound.
In another preferred embodiment, the pharmaceutically acceptable salts include salts formed by combination with inorganic acids, organic acids, alkali metal ions, alkaline earth metal ions, or organic bases capable of providing physiologically acceptable cations, and ammonium salts.
In another preferred embodiment, the mineral acid is selected from hydrochloric acid, hydrobromic acid, phosphoric acid or sulfuric acid; the organic acid is selected from methanesulfonic acid, p-toluenesulfonic acid, trifluoroacetic acid, matrimony vine acid, maleic acid tartaric acid, fumaric acid, citric acid or lactic acid; the alkali metal ions are selected from lithium ions, sodium ions and potassium ions; the alkaline earth metal ions are selected from calcium ions and magnesium ions; the organic base capable of providing a physiologically acceptable cation is selected from methylamine, dimethylamine, trimethylamine, piperidine, morpholine or tris (2-hydroxyethyl) amine.
All such salts within the scope of the present application may be prepared by conventional methods.
The starting materials and intermediates in the preparation of the compounds of the application are readily available and the individual steps can be readily synthesized according to the literature reported or by methods conventional in organic synthesis to those skilled in the art. The compounds of the general formula I may exist in the form of solvates or non-solvates, and crystallization using different solvents may give different solvates.
Preparation method
The present application provides methods for the synthesis of compounds of formula IA and analogs thereof, and pharmaceutically acceptable salts thereof. The synthetic route of the compound is as follows:
the synthesis of the compounds starts from the commercially available starting materials α -naphthalene aldehyde and aminoacetals. Firstly, the compound I1 and the compound I2 are dehydrated under reflux at 100 ℃ to form Schiff base I3 (step 1), the compound I4 is obtained through reductive amination (step 2), the compound I5 is obtained through condensation with Fmoc-protected amino acid (step 3), free primary amine I6 is obtained through removal of Fmoc under diethylamine condition (step 4), the compound I6 is condensed with Fmoc-protected beta alanine to form a compound I7 (step 5), the compound I8 is obtained through ring closure under formic acid condition (step 6), the key intermediate compound I9 is obtained through deprotection (step 7), and the intermediate I9 is reacted with isocyanate to obtain the compound of formula IA (step 8).
Pharmaceutical compositions and methods of administration
Since the compound of the present application has excellent ClpP-modulating activity, the compound of the present application and pharmaceutically acceptable inorganic or organic salts, or stereoisomers thereof, and pharmaceutical compositions containing the compound of the present application as a main active ingredient are useful for preventing and/or treating (stabilizing, alleviating or curing) ClpP-related diseases (e.g., infectious diseases, cancers).
The pharmaceutical compositions of the present application comprise a safe and effective amount of a compound of the present application within a pharmaceutically acceptable excipient or carrier. Wherein "safe and effective amount" means: the amount of the compound is sufficient to significantly improve the condition without causing serious side effects. Typically, the pharmaceutical compositions contain 1-2000mg of the compound of the application per dose, more preferably 10-200mg of the compound of the application per dose. Preferably, the "one dose" is a capsule or tablet.
"pharmaceutically acceptable carrier" means: one or more compatible solid or liquid filler or gel materials which are suitable for human use and must be of sufficient purity and sufficiently low toxicity. "compatible" as used herein means that the components of the composition are capable of blending with and between the compounds of the present application without significantly reducing the efficacy of the compounds. Examples of pharmaceutically acceptable carrier moieties are cellulose and its derivatives (e.g., sodium carboxymethylcellulose, sodium ethylcellulose, cellulose acetate, and the like), gelatin, talc, solid lubricants (e.g., stearic acid, magnesium stearate), calcium sulfate, vegetable oils (e.g., soybean oil, sesame oil, peanut oil, olive oil, and the like), polyols (e.g., propylene glycol, glycerol, mannitol, sorbitol, and the like), emulsifiers (e.g.) Wetting agents (such as sodium lauryl sulfate), coloring agents, flavoring agents, stabilizing agents, antioxidants, preservatives, pyrogen-free water and the like.
The mode of administration of the compounds or pharmaceutical compositions of the present application is not particularly limited, and representative modes of administration include (but are not limited to): oral, parenteral (intravenous, intramuscular or subcutaneous).
Solid dosage forms for oral administration include capsules, tablets, pills, powders and granules. In these solid dosage forms, the active compound is admixed with at least one conventional inert excipient (or carrier), such as sodium citrate or dicalcium phosphate, or with the following ingredients: (a) Fillers or compatibilizers, for example, starch, lactose, sucrose, glucose, mannitol and silicic acid; (b) Binders, for example, hydroxymethyl cellulose, alginate, gelatin, polyvinylpyrrolidone, sucrose and acacia; (c) humectants, e.g., glycerin; (d) Disintegrants, for example, agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain complex silicates, and sodium carbonate; (e) a slow solvent, such as paraffin; (f) an absorption accelerator, e.g., a quaternary amine compound; (g) Wetting agents, such as cetyl alcohol and glycerol monostearate; (h) an adsorbent, for example, kaolin; and (i) a lubricant, for example, talc, calcium stearate, magnesium stearate, solid polyethylene glycol, sodium lauryl sulfate, or mixtures thereof. In capsules, tablets and pills, the dosage forms may also comprise buffering agents.
Solid dosage forms such as tablets, dragees, capsules, pills and granules can be prepared with coatings and shells, such as enteric coatings and other materials well known in the art. They may contain opacifying agents and the release of the active compound or compounds in such compositions may be released in a delayed manner in a certain part of the digestive tract. Examples of embedding components that can be used are polymeric substances and waxes. The active compound may also be in the form of microcapsules with one or more of the above excipients, if desired.
Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, solutions, suspensions, syrups or tinctures. In addition to the active compound, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, propylene glycol, 1, 3-butylene glycol, dimethylformamide and oils, in particular, cottonseed, groundnut, corn germ, olive, castor and sesame oils or mixtures of these substances and the like.
In addition to these inert diluents, the compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
Suspensions, in addition to the active compounds, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum methoxide and agar-agar or mixtures of these substances, and the like.
Compositions for parenteral injection may comprise physiologically acceptable sterile aqueous or anhydrous solutions, dispersions, suspensions or emulsions, and sterile powders for reconstitution into sterile injectable solutions or dispersions. Suitable aqueous and nonaqueous carriers, diluents, solvents or excipients include water, ethanol, polyols and suitable mixtures thereof.
The compounds of the application may be administered alone or in combination with other pharmaceutically acceptable compounds (e.g., other therapeutic agents).
When administered in combination, the pharmaceutical composition also includes one or more (2, 3, 4, or more) other pharmaceutically acceptable compounds. One or more (2, 3, 4, or more) of the other pharmaceutically acceptable compounds may be used simultaneously, separately or sequentially with the compounds of the application for the prevention and/or treatment of ClpP-related diseases.
When a pharmaceutical composition is used, a safe and effective amount of the compound of the present application is applied to a mammal (e.g., a human) in need of treatment, wherein the dose at the time of administration is a pharmaceutically effective dose, and the daily dose is usually 1 to 2000mg, preferably 20 to 500mg, for a human having a body weight of 60 kg. Of course, the particular dosage should also take into account factors such as the route of administration, the health of the patient, etc., which are within the skill of the skilled practitioner.
The main advantages of the application include:
1) The compounds of the application are not structurally modified in the prior literature, but are rationally designed based on the molecular recognition mechanism of ClpP protein and small molecular compounds. The molecular structure of the series of compounds is quite different from the structure reported in the prior art.
2) The compound can effectively regulate ClpP, and has excellent ClpP activating activity and excellent ClpP inhibiting activity;
3) The compound achieves excellent antibacterial effect by adjusting the ClpP target;
4) When the compound is combined with a drug, the compound has remarkable elimination effect on persistent bacteria which are difficult to eliminate by common antibiotic drugs.
The application will be further illustrated with reference to specific examples. It is to be understood that these examples are illustrative of the present application and are not intended to limit the scope of the present application. The experimental methods, in which specific conditions are not noted in the following examples, are generally conducted under conventional conditions or under conditions recommended by the manufacturer. Percentages and parts are weight percentages and parts unless otherwise indicated.
The reagents used in the experiments were all commercially available analytically pure or chemically pure unless specifically indicated and all reagents were purified prior to use.
The column chromatography silica gel is commercial silica gel with 200-300 meshes produced by national pharmaceutical group chemical reagent company; 1 H-NMR, the compounds were isolated using an EZ Plus 100D medium pressure preparation instrument.
EXAMPLE 1 preparation of Compound A26
1. Preparation of Compound 4 (preparation of the remaining intermediate Using the same procedure)
Alpha-naphthalene aldehyde (1.56 g,10.0 mmol) and aminoacetals (1.33 g,10.0 mmol) were heated at 100℃under reflux for 1 hour, cooled to room temperature, diluted with ethanol (25 mL), added sodium borohydride (0.76 g,20 mmol) in portions, and stirred at room temperature for 24 hours. Ethanol was removed by distillation under the reduced pressure, washed with saturated brine, extracted with dichloromethane, and the organic layer was dried by spin-drying and purified by column chromatography (petroleum ether: ethyl acetate=100:5, v: v) to give compound 4.51 g as a yellow oil in 92% yield.
1 H NMR(400MHz,CDCl 3 )δ8.16(d,J＝8.2Hz,1H,ArH),7.89(d,J＝7.8Hz,1H,ArH),7.80(d,J＝8.1Hz,1H,ArH),7.61–7.48(m,3H,ArH),7.45(t,J＝7.3Hz,1H,ArH),4.68(t,J＝4.8Hz,1H,CH),4.29(s,2H,CH 2 Ar),3.78–3.63(m,2H,OCH 2 ),3.60–3.47(m,2H,OCH 2 ),2.90(d,J＝5.1Hz,2H,CH 2 N),1.22(t,J＝7.0Hz,6H,CH 3 ).LC-MS[M+H] + 274.2.
2. Preparation of Compound intermediate 9 (preparation of the remaining intermediates Using the same procedure)
Fmoc-L-isoleucine (0.35 g,1.0 mmol), HOAT (1-hydroxy-7-azabenzotriazole) (0.14 g,1.0 mmol), HATU (2- (7-azabenzotriazol) -N, N, N ', N' -tetramethylurea hexafluorophosphate) (0.46 g,1.2 mmol) and DIPEA (diisopropylethylamine) (0.26 mL,1.5 mmol) were dissolved in DMF (N, N-dimethylformamide) (10 mL), stirred at room temperature for 5 minutes, and after stirring at room temperature for 6 hours, compound 4 (0.27 g,1.0 mmol) was added to the system, washed with water, and extracted with dichloromethane. Dichloroethane was removed by distillation under reduced pressure, DEA (diethylamine) (10 mL) and DCM (dichloromethane) (10 mL) were added to the reaction concentrate, and the mixture was stirred at room temperature overnight. The mixture was spin dried to remove diethylamine and dichloromethane and separated on a normal phase column (petroleum ether: ethyl acetate 2:1, v: v) to give compound 6, LC-MS [ M+H] + 386.3。
Fmoc- β -alanine (217.7 mg,0.7 mmol), HOAT (95.2 mg,0.7 mmol), HATU (319.2 mg,0.84 mmol), DIPEA (0.18 mL,1.05 mmol) and DMF (5 mL) were added to the mixture, and the mixture was stirred at room temperature for 5 min, and Compound 6 was added. The mixture was stirred at room temperature for 6 hours, and the reaction mixture was washed with saturated brine and extracted with dichloromethane. The methylene chloride was distilled off under reduced pressure to give compound 7 as a crude product.
Compound 7 was added to 20mL of a mixed solution of formic acid and methylene chloride (10 mL:10 mL), stirred at room temperature under closed condition for 6-12 hours, LC-MS detection reaction was complete, concentrated by distillation under reduced pressure, diethylamine (10 mL) and methylene chloride (10 mL) were added to the concentrated solution, stirred at room temperature overnight, concentrated, and purified by column chromatography (ethyl acetate: methanol=90:1, v: v) to give compound 9 as whiteColoured solid, yield 76% (410 mg). 1 H NMR(400MHz,CDCl 3 )δ8.13–8.05(m,1H),7.93–7.83(m,2H),7.59–7.50(m,2H),7.45(t,J＝7.5Hz,1H),7.38(d,J＝6.9Hz,1H),5.39(d,J＝14.5Hz,1H),5.30(dd,J＝8.9,6.0Hz,1H),4.81(d,J＝14.5Hz,1H),4.61(dd,J＝9.9,4.1Hz,1H),3.22–3.01(m,3H),3.00–2.91(m,1H),2.46–2.30(m,2H),2.16–2.05(m,1H),1.86(t,J＝9.1Hz,1H),1.60(s,1H),1.50–1.19(m,12H),0.90(t,J＝6.7Hz,3H).
3. Preparation of Compound A26
Compound 9 (73 mg,0.2 mmol) and n-butyl isocyanate (39.7 mg,0.4 mmol) were stirred in dichloromethane (5 mL) overnight, concentrated and isolated compound A26 as a white solid in 81% yield (75 mg) via reverse phase C18 column. 1 H NMR(400MHz,CDCl 3 )δ8.12(d,J＝8.9Hz,1H),7.98–7.80(m,2H),7.55(p,J＝6.9Hz,2H),7.49–7.41(m,1H),7.37(d,J＝6.8Hz,1H),6.07(dd,J＝9.6,5.1Hz,1H),5.26(d,J＝6.1Hz,1H),5.13(dd,J＝35.0,14.6Hz,2H),4.56(s,1H),3.56(dd,J＝14.3,4.6Hz,1H),3.36–3.12(m,5H),2.61–2.49(m,1H),2.36(d,J＝16.8Hz,1H),2.24(dd,J＝6.6,3.5Hz,1H),1.45(dd,J＝14.9,7.3Hz,2H),1.32(td,J＝13.9,6.4Hz,4H),1.14(d,J＝6.8Hz,3H),0.94(dt,J＝14.8,7.3Hz,6H).
The various intermediates and reactants were replaced to give the compounds shown in examples 2-25 below.
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Biological test example 1 enzymatic evaluation of Small molecule agonism of ClpP protease function
Background: the ClpP agonist rearranges the core structure of the ClpP protease by triggering the remodelling of the structure of the ClpP protease complex, so that the protein is separated from the regulation of a normal mechanism, thereby non-specifically degrading a great deal of intracellular functional proteins and inducing bacterial or cancer cell death. For example, an agonist of HsClpP (humanized mitochondrial ClpP) can excite normal proteins in HsClpP nonspecifically degraded cells, so that cancer cells die, and various tumors such as pancreatic cancer, leukemia and the like can be treated. In normal organisms, the function of ClpP depends on the interaction with the chaperone protein ClpX, which depolymerizes misfolded proteins in cells driven by ATP hydrolysis and transfers them into the hydrolysis cavity of ClpP, degrading the proteins and regulating the homeostasis of proteins in normal cells. Inhibitors of ClpP block the interaction of ClpP with ClpX by occupying its binding pocket with chaperone proteins ClpX, thereby making intracellular misfolded proteins difficult to degrade and eliminate, ultimately leading to a range of biological phenotypes. Such as SaClpP (Staphylococcus aureus ClpP) inhibitor, can inhibit the interaction of SaClpP and SaClpX (Staphylococcus aureus ClpX), so that misfolded proteins in bacteria can be accumulated continuously, the production of virulence factors of bacteria can be inhibited, and the virulence of bacteria can be reduced. The compounds of the application can simultaneously inhibit and activate ClpP protease.
Compound agonist activity test method: compound activity assay using alpha-casein (model protein) as substrate, small molecule agonists when combined with ClpP can make ClpP independent of ATP hydrolysis drive ClpX to degrade alpha-casein. Thus, the activity can be further determined by SDS-PAGE. The detection system was 50. Mu.L, 10. Mu.g of HsClpP protein, saClpP or SpClpP (Streptococcus pyogenes ClpP) protein was first dissolved in PD buffer (25 mM HEPES-KOH (pH 7.6), 200mM KCl,5mM MgCl 2 1mM EDTA,10% glycerol and 2mM DTT (dithiothreitol)). After that, the compound was added and incubated at room temperature for 10min, 0.6mg/mL of α -casein was added, and incubated at 37℃for 2 hours, and immediately 12.5. Mu.L of SDS-PAGE loading buffer was added and heated at 100℃for 10min. After SDS-PAGE electrophoresis, coomassie brilliant blue is dyed, decolorized and photographed by using a decolorizing solution, DMSO is used as a negative control, ONC201 and ADEP 4 are used as positive controls, and the activity of the compound for exciting ClpP is judged according to the degradation condition of alpha-casein. The results are shown in Table 1 below.
Compound inhibitory activity test method: GFP-SsrA is a substrate for ClpXP (a protein complex composed of ClpP tetradecmers and ClpX hexamers) interaction, and thus the inhibitory activity of small molecules can be verified by SDS-PAGE. If GFP-SsrA is completely degraded, it indicates that the compound does not possess inhibitory activity, whereas the compound does possess inhibitory activity.
An activity test method of HsClpP small molecule inhibitor. The hydrolysis system was 60. Mu.L, and the reaction was carried out in a solution containing 25mM HEPES-KOH (pH 7.6) and 5mM MgCl 2 In 5mM KCl,0.03% Tween 20, 10% glycerol and 2mM DTT. HsClpP 0.33. Mu.M 14 (HsClpP protein tetradecmer), 0.6. Mu.M HsClpX 6 (HsClpX protein hexamer), 0.4 mg/mL. Alpha. -casein, ATP regenerating system (5 mM ATP,16 mM)CP (creatine phosphate), 0.032mg/mL CK (creatine kinase)), 2mM DTT, and 0.78-100. Mu.M compound. Incubating for 1 hour at 37 ℃, immediately adding 15 mu L of loading buffer, heating for 10min at 100 ℃, performing SDS-PAGE electrophoresis, staining with Coomassie brilliant blue, decolorizing, photographing, archiving, combining with Graphpad drawing, and calculating IC 50 Values.
SaClpP and SpClpP small molecule inhibitor Activity test method. The hydrolysis system was 60. Mu.L PD buffer, 0.33. Mu.M SaClpP 14 (SaClpP protein tetradecmer) or SpClpP 14 (SpClpP protein tetradecmer), 0.6mM SaClpX 6 (SaClpX protein hexamer) or SpClpX 6 (SpClpX protein hexamer), 2. Mu.M GFP-SsrA (substrate for ClpXP interaction), 0.78-100. Mu.M compound. Incubating for 1 hour at 37 ℃, immediately adding 15 mu L of loading buffer, heating for 10min at 100 ℃, performing SDS-PAGE electrophoresis, staining with Coomassie brilliant blue, decolorizing, photographing, archiving, combining with Graphpad drawing, and calculating IC 50 Values, DMSO as negative control, ONC201, ADEP 4 as positive control.
The results are shown in table 1 below:
TABLE 1 results of testing agonistic Activity and inhibitory Activity of Compounds of the application
The results show that the compound provided by the application has excellent agonistic activity and inhibitory activity on ClpP of different species. Among them, a77, a130, a134, a236 showed excellent selectivity against ClpP proteases of different sources.
Biological test example 2 minimum inhibitory concentration experiment (MIC)
Background: the function of the ClpP target protein is related to various biological functions, and researches show that the functional activation and inhibition of the bacterial ClpP protein can influence the survival and virulence of bacteria, and the bacterial sample provided by the embodiment of the application is related to the ClpP target.
Staphylococcus aureus MIC test method: the strain was removed from the-80℃refrigerator and streaked on TSA (trypticase Soy agar medium) plates overnight for 12 hours or more. Picking up5 clinical resistant bacteria NRS-1 (aminoglycoside and tetracycline resistant), NRS-70 (erythromycin resistant), NRS-100 (oxacillin and tetracycline resistant), NRS-108 (gentamicin resistant), NRS-271 (linezolid and ciprofloxacin resistant) and American community acquired resistant Staphylococcus aureus USA300 (methicillin resistant), staphylococcus aureus Newman (sensitive bacteria) were taken in 10mL of TSB (trypticase Soy Broth liquid) medium. The culture was carried out at 37℃and 210rpm overnight, respectively, until the plateau. The following day was diluted 1:1000-fold into fresh TSB medium. Culturing at 37deg.C and 210rpm until OD 600 The bacterial solution was diluted 400-fold with fresh TSB medium at 0.6. The compound is diluted in an equal-fold gradient with fresh TSB culture medium in advance, the final concentration is 0.39-50 mug/ml, diluted bacterial liquid is added into the diluted compound, and then a 96-well plate is placed in a 37 ℃ incubator for static culture for 18 hours. The minimum concentration of the compound that does not inhibit bacterial growth was the MIC value of the compound, as observed visually for bacterial growth in each well. After the compound is obtained in the approximate MIC value range by the primary experiment, the compound is continuously optimized under the secondary condition during the secondary experiment, and finally the optimal MIC value is obtained.
MIC test method of streptococcus pyogenes: the strain is taken out from the refrigerator at the temperature of minus 80 ℃ and then streaked on a TSA plate for culturing overnight for more than 12 hours. A single clone of Streptococcus pyogenes Sp12344 (ATCC Streptococcus pyogenes 12344) obtained in the American type culture Collection was picked in 10mL THB (Todd Hewitt Broth) medium. The culture was carried out at 37℃overnight at 210rpm until the plateau. The following day was diluted 1:1000-fold into fresh THB medium. Culturing at 37deg.C and 210rpm until OD 600 The bacterial solution was diluted 400-fold with fresh THB medium to 0.6. The compounds were diluted in advance with an equal gradient of fresh THB medium to a final concentration of 0.39-50. Mu.g/ml. The diluted bacterial liquid is added into the diluted compound, and then the 96-well plate is placed in a 37 ℃ incubator for static culture for 18 hours. The minimum concentration of the compound that does not inhibit bacterial growth was the MIC value of the compound, as observed visually for bacterial growth in each well. The results are shown in Table 2 below:
TABLE 2 results of minimum inhibitory concentration test of the compounds of the present application
Biological test example 3 test of combination of clinical antibiotics and drugs
Background: in the staphylococcus aureus cultured overnight, most bacteria are killed under the pressure of starvation and the like, partial bacteria become retentive bacteria, the energy in the bacteria is lower, and ClpPX in the bacteria (a certain energy is required for sterilization, and ClpPX cannot play a main role in sterilization) after the ClpPX agonist is combined with traditional antibiotics, such as rifampicin and ciprofloxacin, a large amount of bacteria can be sterilized after the traditional antibiotics are added, but the bacteria have a certain tolerance to the retentive bacteria, and the ClpP small molecule agonist can excite the biological function of the ClpP on the premise of not consuming energy, so that the retentive bacteria are eliminated.
The monoclonal USA300 was picked up in BHI (brain heart infusion medium) medium, incubated at 37℃overnight at 210rpm, 10 mL/tube was aliquoted, 8. Mu.g/mL ciprofloxacin, 0.4. Mu.g/mL rifampicin and 10-fold MIC compound (A28, B29) were added, incubation was continued at 37℃at 210rpm, 100. Mu.L was sampled at different time points 0/24/48/72 hours, centrifugation was carried out for 5 minutes at 12000rpm, the supernatant was discarded, the cells were resuspended in 100. Mu.L of sterile PBS, 10-fold gradient diluted into sterile PBS, and 10. Mu.L of each was plated on MHA (Mueller-Hinton agar). After the bacterial liquid on the flat plate is air-dried, the flat plate is placed at 37 ℃ for inversion culture overnight, and the colony count is recorded on the second day. The graph pad was used to plot the curve.
As shown in figure 1, the antibiotic has no antibacterial effect basically when used singly, and the compound of the application can show excellent combined antibacterial effect when being used together with ciprofloxacin and rifampicin.
All documents mentioned in this disclosure are incorporated by reference in this disclosure as if each were individually incorporated by reference. Further, it will be appreciated that various changes and modifications may be made by those skilled in the art after reading the above teachings, and such equivalents are intended to fall within the scope of the application as defined in the appended claims.

Claims (10)

1. A cyclic peptide compound of formula I:
wherein Y is selected from the group consisting of: n or CR 8 ；
X 1 、X 2 Each independently selected from the group consisting of: o, S, CH 2 Or NH;
l is selected from the group consisting of: H. substituted or unsubstituted C 1 -C 10 Alkyl, -C (O) -A-, -C (O) - (CH) 2 ) p -C(O)-A-、-C(O)NH-A-、-C(O)NH-(CH 2 ) p -C(O)-A-、-C(O)NH-(CH 2 ) p -C(O)O-A-、-S(O) 0-2 -A-, -NHC (O) NH-A-, -C (S) NH-A-, -NHC (S) NH-A-, -C (NH) NH-A-, -NHC (NH) NH-A-; p is selected from the group consisting of: 0.1, 2,3, 4 or 5;
R 1 selected from the group consisting of: H. halogen, unsubstituted C1-C10 alkyl, C1-C4 alkyl substituted with one or more Ra groups (1, 2,3, 4, 5 or more), C1-C4 haloalkyl, C2-C6 alkenyl, C2-C6 alkynyl, C1-C6 alkoxy, C1-C6 alkylthio, -NRbRc, C3-C8 cycloalkyl, C3-C8 heterocyclyl, C5-C8 heteroaryl, unsubstituted C6-C10 aryl, or C6-C10 aryl substituted with one or more Ra groups (1, 2,3, 4, 5 or more); wherein the Ra group is selected from the group consisting of: halogen, C1-C4 haloalkyl (preferably fluoro), C1-C4 alkyl, C1-C4 alkoxy, cyano, amino, or two adjacent Ra groups taken together with the atoms to which they are attached form a C5-C7 carbocyclic or heterocyclic ring; rb, rc are each independently H, C1-C4 alkyl, or Rb, rc together with the atom to which they are attached form a C5-C7 carbocyclic or heterocyclic ring; and when L is-C (O) NH-CH 2 -when R 1 Is not unsubstituted phenyl;
a is selected from unsubstituted C1-C8 alkylene, C1-C4 alkylene substituted with one or more Rd groups, or C1-C8 alkenylene (including monoalkenylene and dienylene); and when L is-C (O) -A-, the Rd group is selected from amino or-NHBoc;
R 2 is a group selected from the group consisting of:
or n-octyl, n-butyl;
wherein R is 7 Selected from the group consisting of: H. CH (CH) 3 、F、Cl、Br、I、OH、SH、NH 2 、CN、CF 3 、OCH 3 、SCH 3 、NHCH 3 、N(CH 3 ) 2 、CHF 2 、OC 2 H 5 、COOH、CONH 2 ；
n=0, 1,2,3, 4, 5, 6, 7, 8, 9, 10; q is selected from the group consisting of: 0.1, 2,3, 4 or 5;
R 3 、R 3 ' each independently selected from the group consisting of: H. halogen, substituted or unsubstituted C1-C4 alkyl, substituted or unsubstituted C2-C6 alkenyl, substituted or unsubstituted C2-C6 alkynyl; or R is 3 And R is 3 ' and the carbon atoms to which they are attached together form a substituted or unsubstituted saturated, partially unsaturated, or aromatic 5-8 membered carbocyclic or heterocyclic ring;
R 8 is H or C1-C4 alkyl, or R 8 And R is R 3 Together forming a C1-C4 alkylene group;
R 4 is thatWherein ring a and ring B are each independently substituted or unsubstituted saturated, partially unsaturated, or aromatic 5-14 membered carbocycle or heterocycle (including monocyclic, fused or spiro), and ring a and ring B are fused to form a polycyclic fused ring; wherein R is 4 Optionally substituted by Re selected from halogen, C1-C4 alkyl, C1-C4 alkoxy;
R 5 selected from H, C1-C4 alkyl;
when each CH is 2 And NH, alone or as part of another group, may be optionally substituted;
unless specifically stated otherwise, the term "substituted" means that one or more hydrogen atoms on the group are replaced with a substituent selected from the group consisting of: halogen, oxo, carboxyl, cyano, hydroxyl, phenyl, 5-6 membered heterocyclyl, C1-C6 alkyl, C1-C6 alkoxy, C3-C8 cycloalkyl substitution, amino, N-dimethylamino, mercapto, C 1 -C 6 And (3) sulfonyl.
2. The compound of claim 1, or a pharmaceutically acceptable salt or stereoisomer thereof, wherein the compound has the structure of formula II:
wherein X is 3 Selected from O or S;
X 1 、X 2 、R 1 、R 2 、R 3 、R 3 ’、R 4 、R 5 y, A are as claimed in claim 1.
3. A compound according to claim 1 or claim 2, or a pharmaceutically acceptable salt or stereoisomer thereof, wherein Y is N and X is 1 、X 2 Each independently is O.
4. The compound of claim 1 or 2, or a pharmaceutically acceptable salt or stereoisomer thereof, wherein R 1 Selected from H, halogen, unsubstituted C1-C10 alkyl, C1-C4 haloalkyl, C3-C8 cycloalkyl, C3-C8 heterocyclyl, unsubstituted C6-C10 aryl, or C6-C10 aryl substituted with one or more Ra groups (1, 2,3, 4, 5, or more);
wherein the Ra group is selected from the group consisting of: halogen, C1-C4 haloalkyl (preferably fluoro), C1-C4 alkyl, C1-C4 alkoxy, cyano, amino, or two adjacent Ra groups taken together with the atoms to which they are attached form a 5-7 membered carbocyclic or heterocyclic ring; and when L is-C (O) NH-A-, R 1 Not unsubstituted phenyl.
5. The compound of claim 1 or 2, or a pharmaceutically acceptable salt or stereoisomer thereof, wherein R 2 Is a group selected from the group consisting of:
wherein R is 7 Selected from the group consisting of: H. CH (CH) 3 、F、Cl、Br、I、OH、SH、NH 2 、CN、CF 3 、OCH 3 、SCH 3 、NHCH 3 、N(CH 3 ) 2 、CHF 2 、OC 2 H 5 、COOH、CONH 2 ；
n=0, 1,2 or 3; q is selected from the group consisting of: 0.1, 2,3, 4 or 5.
6. The compound of claim 1 or 2, or a pharmaceutically acceptable salt or stereoisomer thereof, wherein R 4 Is thatWherein ring a and ring B are each independently a substituted or unsubstituted aromatic 5-14 membered carbocyclic or heterocyclic ring (including monocyclic, fused or spiro ring), and ring a and ring B are fused to form a bicyclic fused or tricyclic fused ring.
7. The compound of claim 1, or a pharmaceutically acceptable salt or stereoisomer thereof, wherein the compound of formula I is selected from the group consisting of:
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8. a compound, or a pharmaceutically acceptable salt or stereoisomer thereof, wherein the compound is selected from the group consisting of:
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9. a pharmaceutical composition comprising the following components:
1) A therapeutically effective amount of one or more compounds of claim 1 or 8, or a pharmaceutically acceptable salt or stereoisomer thereof;
2) A pharmaceutically acceptable carrier or excipient; and
3) Optionally a second therapeutic agent, said second therapeutic agent being an antibacterial agent.
10. Use of a compound according to claim 1 or 8, or a pharmaceutically acceptable salt or stereoisomer thereof, for the preparation of a pharmaceutical composition for the prevention and/or treatment of a disease or condition associated with ClpP protease activity or expression level.
CN202210377247.XA 2022-04-11 2022-04-11 Cyclic peptide compound and application thereof Pending CN116925081A (en)

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WO2003031448A1 (en) * 2001-10-12 2003-04-17 Choongwae Pharma Corporation Reverse-turn mimetics and method relating thereto
US7576084B2 (en) * 2001-10-12 2009-08-18 Choongwae Pharma Corporation Reverse-turn mimetics and method relating thereto
US6762185B1 (en) * 2002-03-01 2004-07-13 Choongwae Pharma Corporation Compounds useful for treatment of cancer, compositions containing the same, and methods of their use
AU2003284120A1 (en) * 2002-10-17 2004-05-04 Myriad Genetics, Inc. Reverse-turn mimetics and composition and methods relating thereto
NZ545568A (en) * 2003-08-28 2009-06-26 Choongwae Pharma Corp Use of compounds that modulate beta-catenin/TCF activated transcription for manufacture of a medicamnet to treat cancer
US20140051706A1 (en) * 2011-02-25 2014-02-20 Prism Pharma Co., Ltd. Alpha helix mimetics and methods relating thereto
ES2660756T3 (en) * 2011-04-15 2018-03-26 National University Corporation Tottori University Synthesis and analysis of new compounds capable of inducing differentiation of human mesenchymal stem cell in hepatocyte
CN106132417B (en) * 2014-03-28 2020-04-14 国立大学法人鸟取大学 Cancer and fibrosis inhibiting effects of low molecular weight compound
JP6785487B2 (en) * 2015-09-18 2020-11-18 国立大学法人鳥取大学 Effect of low molecular weight compounds to suppress cancer and fibrosis and promote regeneration

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