WO2013173393A1 - Drug-conjugates, conjugation methods, and uses thereof - Google Patents

Drug-conjugates, conjugation methods, and uses thereof Download PDF

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Publication number
WO2013173393A1
WO2013173393A1 PCT/US2013/041028 US2013041028W WO2013173393A1 WO 2013173393 A1 WO2013173393 A1 WO 2013173393A1 US 2013041028 W US2013041028 W US 2013041028W WO 2013173393 A1 WO2013173393 A1 WO 2013173393A1
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WIPO (PCT)
Prior art keywords
optionally substituted
compound
alkyl
group
hydrogen
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PCT/US2013/041028
Other languages
French (fr)
Inventor
Zhenwei Miao
Yufeng Hong
Tong Zhu
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Concortis Biosystems, Corp
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Application filed by Concortis Biosystems, Corp filed Critical Concortis Biosystems, Corp
Priority to US14/401,318 priority Critical patent/US9801951B2/en
Priority to EP13790334.0A priority patent/EP2849797B1/en
Priority to CN201380025785.1A priority patent/CN104640572B/en
Priority to JP2015512771A priority patent/JP6280103B2/en
Publication of WO2013173393A1 publication Critical patent/WO2013173393A1/en
Priority to HK15108781.9A priority patent/HK1208163A1/en
Priority to US15/679,599 priority patent/US20180085471A1/en

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    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
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    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
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    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A61K47/6811—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates the drug being a protein or peptide, e.g. transferrin or bleomycin
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    • A61K47/6889—Conjugates wherein the antibody being the modifying agent and wherein the linker, binder or spacer confers particular properties to the conjugates, e.g. peptidic enzyme-labile linkers or acid-labile linkers, providing for an acid-labile immuno conjugate wherein the drug may be released from its antibody conjugated part in an acidic, e.g. tumoural or environment
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    • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
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    • C07D207/02—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D207/04—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members
    • C07D207/08—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members with hydrocarbon radicals, substituted by hetero atoms, attached to ring carbon atoms
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    • C07D207/04—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members
    • C07D207/08—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members with hydrocarbon radicals, substituted by hetero atoms, attached to ring carbon atoms
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    • C07K5/00—Peptides containing up to four amino acids in a fully defined sequence; Derivatives thereof
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Definitions

  • Cytotoxic agents can provide therapeutic benefits in the treatment of various conditions, including various cancers. Accordingly, it is desirable to provide cytotoxic agents with therapeutically useful properties, for example, as chemotherapies in cancer treatments.
  • cytotoxic agents as chemotherapies usually develop drug resistances, and thus, drop their therapeutic efficacies. Accordingly, it is desirable to provide cytotoxic agents with improved drug resistance profiles.
  • One possibility is to design cytotoxic compounds with efflux pump resistances.
  • Another possibility is to design cytotoxic compounds potentially act on more than one targets.
  • Tubulins are a class of targets for anti-mitotic agents as chemotherapies alone or in combination with other chemotherapies or as active agent-conjugates.
  • Examples of Tubulin-B hidin Agents include, but are not limited to, the following compounds:
  • Proteasome inhibitors include, but are not limited to, the following compounds:
  • MMP Inhibitors examples include, not limited to:
  • Some embodiments provide compounds, methods of preparing compounds, and uses thereof.
  • Some embodiments provide compound-conjugates, methods of preparing compound-conjugates, and uses thereof.
  • Some embodiments provide a compound having the structure of Formula
  • Some embodiments provide a compound having the structure of Formula la:
  • B is a moiety might have contribution to enzyme inhibition or efflux pump resistance
  • R 1 -R.8 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R 7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • the compound having the structure of Formula I has the structure of F
  • B is a moiety might have contribution to enzyme inhibition or efflux pump resistance
  • Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R 3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R 7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • Z is -F, -SR, -N 3 , -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-C 8 alkyl or substituted Ci-C 8 alkyl.
  • Some embodiments provide a compound having the structure of Formula
  • X is OR 10 , selected from, but not limited to, a group consisting of at least one hetero atom:
  • X is S0 2 R 10 , selected from, but not limited to, a group consisting of at least one hetero atom:
  • R 1 -R 10 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally and respectively R 7 , Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • X is a group consisting of at least one heteroatom
  • the dual active compound having the structure of Formula I has the structure of Formula lib:
  • n 0 or 1;
  • X is OR 10 , selected from, but not limited to, a group consisting of at least one hetero atom:
  • n 0 or 1;
  • X is S0 2 R 10 , selected from, but not limited to, a group consisting of at least one hetero atom:
  • R 1 -R 10 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally and respectively R 7 , Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • X is a group of at least one heteroatom
  • Z is -F, -SR, -N 3 , -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-Cg alkyl or substituted Ci-Cg alkyl.
  • R 1 and R 2 together with the nitrogen to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R 1 and R 3 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R 7 and R 8 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7- membered ring, or optionally R 1 is R 1A or R 1B ;
  • R 1A comprises a targeting moiety
  • R 1B is -L 1 (CH 2 ) n R c , -L 1 0(CH 2 ) n R c or -(CH 2 ) n R c ;
  • R is Ci-Cg alkyl, C 3 -Cg cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R , or optionally R comprises a targeting moiety;
  • each NR E R F is independently selected, wherein R E and R F are each independently selected from hydrogen, -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]- [L 1 (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ] s -(L 1 ) s -R J , -[(i MQR ⁇ NR ⁇ MQR 2 ⁇ ),.]- (L 1 ) s [(C(R 2A ) 2 ) r O(C(R 2A ) 2 ) r (L 2 ) s ] s -(L 1 ) s -R J , optionally substituted C 1-8 alkyl, optionally substituted C 3 _ 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and
  • each R H is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or -NR E R F ;
  • each NR R is independently selected, wherein each R is independently selected from the group consisting of hydrogen, -OH, optionally substituted Ci-Cg alkyl, optionally substituted C 3 -Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, or optionally both R together with the nitrogen to which they are attached are an optionally substituted heterocyclyl;
  • each R 2F is independently selected from the group consisting hydrogen, optionally substituted Ci-C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
  • each L 2 is independently selected from the group consisting of optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
  • each m independently is 1 or 2;
  • each n independently is 0, 1, 2, 3, 4, 5, or 6;
  • each r independently is 0, 1, 2, 3, 4, 5, or 6;
  • each s independently is 0 or 1 ;
  • each z independently is 1 or 2
  • R 7 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C 3 -Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
  • R 8 is selected from the group consisting of H (hydrogen), -(CH 2 ) utilizatR C , optionally substituted Ci-C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
  • E is selected from the roup consisting of:
  • H hydrogen
  • Ci-Cg alkyl optionally substituted Ci-Cg alkoxy
  • C 3 -C 8 cycloalkyl optionally substituted aryl, and optionally substituted heteroaryl
  • Figures 1-10 shows the cytotoxic effects of compounds or antibody drug conjugates (ADCs) on various cell types.
  • the antibody used in the antibody drug conjugates is Trastuzumab.
  • Some embodiments provide a compound.
  • the compound includes a linker.
  • the compound includes a cytotoxic agent.
  • the compound includes a functional group that has tubulin-binding properties or tubulin inhibitory properties.
  • the compound includes a functional group that has protease inhibitory or efflux pump resistant properties.
  • the functional group may have proteasome inhibitory properties.
  • pharmaceutically acceptable salt refers to salts that retain the biological effectiveness and properties of a compound and, which are not biologically or otherwise undesirable for use in a pharmaceutical.
  • the compounds disclosed herein are capable of forming acid and/or base salts by virtue of the presence of amino and/or carboxyl groups or groups similar thereto.
  • Pharmaceutically acceptable acid addition salts can be formed with inorganic acids and organic acids. Inorganic acids from which salts can be derived include, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like.
  • Organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like.
  • Pharmaceutically acceptable base addition salts can be formed with inorganic and organic bases.
  • Inorganic bases from which salts can be derived include, for example, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum, and the like; particularly preferred are the ammonium, potassium, sodium, calcium and magnesium salts.
  • Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, basic ion exchange resins, and the like, specifically such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine. Many such salts are known in the art, as described in WO 87/05297, Johnston et al, published September 11 , 1987 (incorporated by reference herein in its entirety).
  • C a to C b “ or “C a _ b “ in which "a” and “b” are integers refer to the number of carbon atoms in the specified group. That is, the group can contain from “a” to “b", inclusive, carbon atoms.
  • a “Ci to C 4 alkyl” or “Ci_ 4 alkyl” group refers to all alkyl groups having from 1 to 4 carbons, that is, CH 3 -, CH 3 CH 2 -, CH 3 CH 2 CH 2 -, (CH 3 ) 2 CH-, CH 3 CH 2 CH 2 CH 2 -, CH 3 CH 2 CH(CH 3 )- and (CH 3 ) 3 C-.
  • halogen or "halo,” as used herein, means any one of the radio- stable atoms of column 7 of the Periodic Table of the Elements, e.g., fluorine, chlorine, bromine, or iodine, with fluorine and chlorine being preferred.
  • alkyl refers to a straight or branched hydrocarbon chain that is fully saturated (i.e., contains no double or triple bonds).
  • the alkyl group may have 1 to 20 carbon atoms (whenever it appears herein, a numerical range such as “1 to 20" refers to each integer in the given range; e.g., "1 to 20 carbon atoms” means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 20 carbon atoms, although the present definition also covers the occurrence of the term "alkyl” where no numerical range is designated).
  • the alkyl group may also be a medium size alkyl having 1 to 9 carbon atoms.
  • the alkyl group could also be a lower alkyl having 1 to 4 carbon atoms.
  • the alkyl group may be designated as "Ci_ 4 alkyl” or similar designations.
  • “Ci_ 4 alkyl” indicates that there are one to four carbon atoms in the alkyl chain, i.e., the alkyl chain is selected from the group consisting of methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl.
  • Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, hexyl, and the like.
  • alkoxy refers to the formula -OR wherein R is an alkyl as is defined above, such as “Ci_9 alkoxy”, including but not limited to methoxy, ethoxy, n- propoxy, 1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy, sec-butoxy, and tert-butoxy, and the like.
  • alkylthio refers to the formula -SR wherein R is an alkyl as is defined above, such as "Ci_9 alkylthio” and the like, including but not limited to methylmercapto, ethylmercapto, n-propylmercapto, 1-methylethylmercapto (isopropylmercapto), n-butylmercapto, iso-butylmercapto, sec-butylmercapto, tert- butylmercapto, and the like.
  • alkenyl refers to a straight or branched hydrocarbon chain containing one or more double bonds.
  • the alkenyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term "alkenyl” where no numerical range is designated.
  • the alkenyl group may also be a medium size alkenyl having 2 to 9 carbon atoms.
  • the alkenyl group could also be a lower alkenyl having 2 to 4 carbon atoms.
  • the alkenyl group may be designated as "C2-4 alkenyl" or similar designations.
  • C2-4 alkenyl indicates that there are two to four carbon atoms in the alkenyl chain, i.e., the alkenyl chain is selected from the group consisting of ethenyl, propen-l-yl, propen-2-yl, propen-3-yl, buten-l-yl, buten-2-yl, buten-3-yl, buten- 4-yl, 1-methyl-propen-l-yl, 2-methyl-propen-l-yl, 1-ethyl-ethen-l-yl, 2-methyl-propen-3-yl, buta-l,3-dienyl, buta-l,2,-dienyl, and buta-l,2-dien-4-yl.
  • Typical alkenyl groups include, but are in no way limited to, ethenyl, propenyl, butenyl, pentenyl, and hexenyl, and the like.
  • alkynyl refers to a straight or branched hydrocarbon chain containing one or more triple bonds.
  • the alkynyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term "alkynyl” where no numerical range is designated.
  • the alkynyl group may also be a medium size alkynyl having 2 to 9 carbon atoms.
  • the alkynyl group could also be a lower alkynyl having 2 to 4 carbon atoms.
  • the alkynyl group may be designated as "C 2 - 4 alkynyl" or similar designations.
  • C 2 - 4 alkynyl indicates that there are two to four carbon atoms in the alkynyl chain, i.e., the alkynyl chain is selected from the group consisting of ethynyl, propyn-l-yl, propyn-2-yl, butyn-l-yl, butyn-3-yl, butyn-4-yl, and 2- butynyl.
  • Typical alkynyl groups include, but are in no way limited to, ethynyl, propynyl, butynyl, pentynyl, and hexynyl, and the like.
  • aromatic refers to a ring or ring system having a conjugated pi electron system and includes both carbocyclic aromatic (e.g., phenyl) and heterocyclic aromatic groups (e.g., pyridine).
  • carbocyclic aromatic e.g., phenyl
  • heterocyclic aromatic groups e.g., pyridine
  • the term includes monocyclic or fused-ring polycyclic (i.e., rings which share adjacent pairs of atoms) groups provided that the entire ring system is aromatic.
  • aryloxy and arylthio refers to RO- and RS-, in which R is an aryl as is defined above, such as “C 6 -io aryloxy” or “C 6 -io arylthio” and the like, including but not limited to phenyloxy.
  • an "aralkyl” or “arylalkyl” is an aryl group connected, as a substituent, via an alkylene group, such as "C7_i 4 aralkyl” and the like, including but not limited to benzyl, 2- phenylethyl, 3-phenylpropyl, and naphthylalkyl.
  • the alkylene group is a lower alkylene group (i.e., a Ci_ 4 alkylene group).
  • heteroaryl refers to an aromatic ring or ring system (i.e., two or more fused rings that share two adjacent atoms) that contain(s) one or more heteroatoms, that is, an element other than carbon, including but not limited to, nitrogen, oxygen and sulfur, in the ring backbone.
  • heteroaryl is a ring system, every ring in the system is aromatic.
  • the heteroaryl group may have 5-18 ring members (i.e., the number of atoms making up the ring backbone, including carbon atoms and heteroatoms), although the present definition also covers the occurrence of the term "heteroaryl" where no numerical range is designated.
  • the heteroaryl group has 5 to 10 ring members or 5 to 7 ring members.
  • the heteroaryl group may be designated as "5-7 membered heteroaryl,” "5-10 membered heteroaryl,” or similar designations.
  • heteroaryl rings include, but are not limited to, furyl, thienyl, phthalazinyl, pyrrolyl, oxazolyl, thiazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, triazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, quinolinyl, isoquinlinyl, benzimidazolyl, benzoxazolyl, benzothiazolyl, indolyl, isoindolyl, and benzothienyl.
  • a “heteroaralkyl” or “heteroarylalkyl” is heteroaryl group connected, as a substituent, via an alkylene group. Examples include but are not limited to 2-thienylmethyl, 3-thienylmethyl, furylmethyl, thienylethyl, pyrrolylalkyl, pyridylalkyl, isoxazollylalkyl, and imidazolylalkyl.
  • the alkylene group is a lower alkylene group (i.e., a Ci_ 4 alkylene group).
  • carbocyclyl means a non-aromatic cyclic ring or ring system containing only carbon atoms in the ring system backbone.
  • carbocyclyl is a ring system, two or more rings may be joined together in a fused, bridged or spiro-connected fashion.
  • Carbocyclyls may have any degree of saturation provided that at least one ring in a ring system is not aromatic.
  • carbocyclyls include cycloalkyls, cycloalkenyls, and cycloalkynyls.
  • the carbocyclyl group may have 3 to 20 carbon atoms, although the present definition also covers the occurrence of the term "carbocyclyl” where no numerical range is designated.
  • the carbocyclyl group may also be a medium size carbocyclyl having 3 to 10 carbon atoms.
  • the carbocyclyl group could also be a carbocyclyl having 3 to 6 carbon atoms.
  • the carbocyclyl group may be designated as "C3-6 carbocyclyl" or similar designations.
  • carbocyclyl rings include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclohexenyl, 2,3-dihydro-indene, bicycle[2.2.2]octanyl, adamantyl, and spiro[4.4]nonanyl.
  • a "(carbocyclyl)alkyl” is a carbocyclyl group connected, as a substituent, via an alkylene group, such as "C 4 _io (carbocyclyl)alkyl” and the like, including but not limited to, cyclopropylmethyl, cyclobutylmethyl, cyclopropylethyl, cyclopropylbutyl, cyclobutylethyl, cyclopropylisopropyl, cyclopentylmethyl, cyclopentylethyl, cyclohexylmethyl, cyclohexylethyl, cycloheptylmethyl, and the like.
  • the alkylene group is a lower alkylene group.
  • cycloalkyl means a fully saturated carbocyclyl ring or ring system. Examples include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
  • cycloalkenyl means a carbocyclyl ring or ring system having at least one double bond, wherein no ring in the ring system is aromatic.
  • An example is cyclohexenyl.
  • heterocyclyl means a non-aromatic cyclic ring or ring system containing at least one heteroatom in the ring backbone. Heterocyclyls may be joined together in a fused, bridged or spiro-connected fashion. Heterocyclyls may have any degree of saturation provided that at least one ring in the ring system is not aromatic. The heteroatom(s) may be present in either a non-aromatic or aromatic ring in the ring system.
  • the heterocyclyl group may have 3 to 20 ring members (i.e., the number of atoms making up the ring backbone, including carbon atoms and heteroatoms), although the present definition also covers the occurrence of the term "heterocyclyl” where no numerical range is designated.
  • the heterocyclyl group may also be a medium size heterocyclyl having 3 to 10 ring members.
  • the heterocyclyl group could also be a heterocyclyl having 3 to 6 ring members.
  • the heterocyclyl group may be designated as "3-6 membered heterocyclyl" or similar designations.
  • the heteroatom(s) are selected from one up to three of O, N or S, and in preferred five membered monocyclic heterocyclyls, the heteroatom(s) are selected from one or two heteroatoms selected from O, N, or S.
  • heterocyclyl rings include, but are not limited to, azepinyl, acridinyl, carbazolyl, cinnolinyl, dioxolanyl, imidazolinyl, imidazolidinyl, morpholinyl, oxiranyl, oxepanyl, thiepanyl, piperidinyl, piperazinyl, dioxopiperazinyl, pyrrolidinyl, pyrrolidonyl, pyrrolidionyl, 4-piperidonyl, pyrazolinyl, pyrazolidinyl, 1,3-dioxinyl, 1,3-dioxanyl, 1,4- dioxinyl, 1 ,4-dioxanyl, 1,3-oxathianyl, 1 ,4-oxathianyl, 2H-l,2-oxazinyl, trioxanyl
  • a "(heterocyclyl)alkyl” is a heterocyclyl group connected, as a substituent, via an alkylene group. Examples include, but are not limited to, imidazolinylmethyl and indolinylethyl.
  • Non- limiting examples include formyl, acetyl, propanoyl, benzoyl, and acryl.
  • R is selected from hydrogen, Ci_ 6 alkyl, C 2 _ 6 alkenyl, C 2 _ 6 alkynyl, C 3 -7 carbocyclyl, C 6 -io aryl, 5- 10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
  • a "cyano" group refers to a "-CN” group.
  • a "cyanato” group refers to an "-OCN” group.
  • An "isocyanato” group refers to a "-NCO” group.
  • a "thiocyanato" group refers to a "-SCN” group.
  • An “isothiocyanato” group refers to an "-NCS” group.
  • a “sulfonyl” group refers to an "-S0 2 R” group in which R is selected from hydrogen, Ci_ 6 alkyl, C 2 _ 6 alkenyl, C 2 _ 6 alkynyl, C 3 _ 7 carbocyclyl, C 6 _io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
  • S-sulfonamido refers to a "-S0 2 NR A RB” group in which R A and R B are each independently selected from hydrogen, Ci_ 6 alkyl, C 2 _ 6 alkenyl, C 2 _ 6 alkynyl, C3-7 carbocyclyl, C 6 -io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
  • N-sulfonamido refers to a "-N(R A )S0 2 R B " group in which R A and R b are each independently selected from hydrogen, Ci_ 6 alkyl, C 2 _ 6 alkenyl, C 2 _ 6 alkynyl, C 3 _7 carbocyclyl, C 6 _io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
  • An “amino” group refers to a "-NR A R B " group in which R A and R B are each independently selected from hydrogen, Ci_ 6 alkyl, C 2 _ 6 alkenyl, C 2 _ 6 alkynyl, C 3 _ 7 carbocyclyl, C 6 -io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
  • a non- limiting example includes free amino (i.e., -NH 2 ).
  • An “aminoalkyl” group refers to an amino group connected via an alkylene group.
  • alkoxyalkyl refers to an alkoxy group connected via an alkylene group, such as a “C 2 -8 alkoxyalkyl” and the like.
  • a substituted group is derived from the unsubstituted parent group in which there has been an exchange of one or more hydrogen atoms for another atom or group.
  • substituted it is meant that the group is substituted with one or more subsitutents independently selected from Ci-C 6 alkyl, C 2 -C6 alkenyl, C 2 -C6 alkynyl, C3-C7 carbocyclyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), C 3 -C 7 -carbocyclyl- Ci-C 6 -alkyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy),
  • radical naming conventions can include either a mono-radical or a di-radical, depending on the context.
  • a substituent requires two points of attachment to the rest of the molecule, it is understood that the substituent is a di-radical.
  • a substituent identified as alkyl that requires two points of attachment includes di-radicals such as -CH 2 -, -CH 2 CH 2 -, -CH 2 CH(CFi3)CFi 2 -, and the like.
  • Other radical naming conventions clearly indicate that the radical is a di-radical such as "alkylene” or "alkenylene.”
  • R groups are said to form a ring (e.g., a carbocyclyl, heterocyclyl, aryl, or heteroaryl ring) "together with the atom to which they are attached," it is meant that the collective unit of the atom and the two R groups are the recited ring.
  • the ring is not otherwise limited by the definition of each R group when taken individually. For example, when the following substructure is present:
  • R 1 and R 2 are defined as selected from the group consisting of hydrogen and alkyl, or R 1 and R 2 together with the nitrogen to which they are attached form a heterocyclyl, it is meant that R 1 and R 2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure:
  • ring E is a heteroaryl ring containing the depicted nitrogen.
  • R 1 and R 2 are defined as selected from the group consisting of hydrogen and alkyl, or R 1 and R 2 together with the atoms to which they are attached form an aryl or carbocylyl, it is meant that R 1 and R 2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure:
  • E is an aryl ring or a carbocylyl containing the depicted double bond.
  • a substituent is depicted as a di-radical (i.e., has two points of attachment to the rest of the molecule), it is to be understood that the substituent can be attached in any directional configuration unless otherwise indicated.
  • a substituent depicted as -AE- or v 3 ⁇ 4 A ⁇ E A includes the substituent being oriented such that the A is attached at the leftmost attachment point of the molecule as well as the case in which A is attached at the rightmost attachment point of the molecule.
  • Subject as used herein, means a human or a non-human mammal, e.g., a dog, a cat, a mouse, a rat, a cow, a sheep, a pig, a goat, a non-human primate or a bird, e.g., a chicken, as well as any other vertebrate or invertebrate.
  • Isotopes may be present in the compounds described. Each chemical element present in a compound either specifically or generically described hereinmay include any isotope of said element.
  • a hydrogen atom may be explicitly disclosed or understood to be present in the compound and each such hydrogen atom is any isotope of hydrogen, including but not limited to hydrogen-1 (protium) and hydrogen-2 (deuterium).
  • reference herein to a compound encompasses all potential isotopic forms unless the context clearly dictates otherwise.
  • Some embodiments provide a method of treating a patient in need thereof comprising administering a compound as disclosed and described herein to said patient.
  • the patient may have cancer, an infection, or an immune system disease.
  • the compound may have anti-tumor, antibiotic, or anti-inflammatory activity.
  • Some embodiments provide a compound having the structure
  • A is a tubulin binding moiety
  • B is a group might have protease inhibitory or efflux pump resistant properties
  • Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, substituted or cyclic Ci-Cg alkyl, aryl, and substituted aryl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally R 7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring.
  • the compound may be used alone as API (active pharmaceutical ingredient) or in a prodrug form.
  • the compound may be included in a conjugate including a linker and another component.
  • the compound may be included in a conjugate including a linker and a targeting moiety, such as antibody, Fab, peptide, protein ligand, and the like.
  • the compound may be included in a conjugate including a linker and a carrier molecule, such as HSA, lipid, polymers, nanoparticles, and the like.
  • the compound may be included in a conjugate including a linker and a small molecule drug/ligand, such as folic acid.
  • tubulin binding moiety refers to a structural component of a compound that inhibits tubulin polymerization under a certain set of conditions.
  • the compound may inhibit tubulin polymerization under in vivo or in vitro conditions.
  • the compound may inhibit tubulin polymerization in PBS. Examples of compounds that inhibit tubulin polymerization are described in Peltier, et al, "The Total Synthesis of Tubulysin D," J. Am. Chem. Soc, 2006, 128 (50): 16018-16019, and U.S. Publication No.: 2005/0239713 the disclosures of which are incorporated herein by reference in their entirety.
  • the term "functional moiety” refers to a structural component of a compound that interacts with a biological moiety or fragment of the biological moiety under a certain set of conditions.
  • the functional moiety may interact with a biological moiety or fragment of the biological moiety under in vivo or in vitro conditions.
  • the functional moiety may interact with a biological moiety or fragment of the biological moiety in PBS.
  • the functional moiety may afford a desirable effect in a compound comparison to a compound that does not include the functional moiety.
  • the functional moiety may contribute to enzyme inhibition or efflux pump resistance in a compound.
  • the cytotoxic compound having the structure of Formula la having the structure of Formula la:
  • B is a moiety might have contribution to enzyme inhibition or efflux pump resistance
  • Ri-R.8 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R 7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • the dual active compound having the structure of Formula I has the structure of Formula lb:
  • B is a moiety might have contribution to enzyme inhibition or efflux pump resistance
  • Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R 7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • Z is -F, -SR, -N 3 , -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-Cg alkyl or substituted Ci-Cg alkyl
  • X is OR 10 , selected from, but not limited to, a group consisting of at least one hetero atom:
  • Ri-Rio are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, , or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally and respectively R 7 , Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • X is a group consisting of at least one heteroatom
  • the dual active compound having the structure of Formula I has the structure of Formula lib:
  • n 0 or 1 ;
  • X is OR 10 , selected from, but not limited to, a group consisting of at least one hetero atom:
  • n is 0 or 1 ;
  • XX i is S0 2 R , selected from, but not limited to, a group consistin of at least one hetero atom:
  • Ri-Rio are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally and respectively R 7 , Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
  • X is a group of at least one heteroatom
  • Z is -F, -SR, -N 3 , -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-C 8 alkyl or substituted Ci-C 8 alkyl
  • Examples of compounds having the structure of Formula la include but not limited to the following:
  • Examples of compounds having the structure of Formula la include the following:
  • Examples of general compounds having the structure of Formula la include the following:
  • Examples of compounds having the structure of Formula la include the following:
  • Examples of general compounds having the structure of Formula la include the following:
  • Examples of compounds having the structure of Formula la include the following:
  • Examples of general compounds having the structure of Formula la include the following:
  • Examples of compounds having the structure of Formula la include the following:
  • Examples of general compounds having the structure of Formula la include the following: H
  • Examples of compounds having the structure of Formula la include the following:
  • Examples of general compounds having the structure of Formula la include the following:
  • Examples of compounds having the structure of Formula lb include the following:
  • Examples of compounds having the structure of Formula lb include the following:
  • the compound is conjugated to a targeting moiety.
  • the targeting moiety includes a monoclonal antibody (mAB).
  • the compound includes a spacer or a multifunctional linker.
  • the spacer connects to the mAB by a group including a N (nitrogen) atom.
  • the multifunctional linker connects to the mAB by a group including a N (nitrogen) atom.
  • the spacer or multifunctional linker may be optionally connected to an auxiliary moiety.
  • the auxiliary moiety may be a second targeting moiety such as mAB and peptide.
  • the auxiliary moiety may be a hydrophilic polymer such as polyethylene glycol (PEG), and the like.
  • the spacer or multifunctional linker may include a group including a N (nitrogen) atom.
  • the spacer or multifunctional linker may include a cyclic group including a N (nitrogen) atom.
  • the spacer connects to the mAB by a sulfide bond.
  • the multifunctional linker connects to the mAB by a sulfide bond.
  • the spacer or multifunctional linker may be optionally connected to an auxiliary moiety.
  • the auxiliary moiety may be a second targeting moiety such as mAB and peptide.
  • the auxiliary moiety may be a hydrophilic polymer such as polyethylene glycol (PEG), and the like.
  • the spacer or multifunctional linker may include a 2- to 5- atom bridge.
  • the spacer or multifunctional linker may include a 4C bridge.
  • Some embodiments provide a method of conjugating of a targeting moiety through a spacer or a multifunctional linker.
  • the spacer or multifunctional linker may include a 2- to 5- atom bridge.
  • the method includes a single-step or sequential conjugation approach.
  • the compound includes a spacer or a multifunctional linker.
  • the spacer or multifunctional linker may include a noncleavable or cleavable unit such as peptides.
  • the spacer or multifunctional linker may include a group including a N (nitrogen) atom.
  • the method includes a single- step or sequential conjugation approach.
  • the spacer or multifunctional linker may include a noncleavable or cleavable unit such as a peptide.
  • Some embodiments provide a compound-conjugate having the structure of Formula Ila:
  • R ⁇ R 9 are each independently selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl, or optionally R 1 and R 2 together with the nitrogen to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R 1 and R 3 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7- membered ring, or optionally R 7 , R 8 and R 9 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R 1 is R 1A or R 1B ;
  • R 1A comprises a targeting moiety
  • R 1B is -L 1 (CH 2 ) n R c , -L 1 0(CH 2 ) n R c or -(CH 2 ) n R c ;
  • R is Ci-Cg alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R , or optionally R comprises a targeting moiety;
  • each NR E R F is independently selected, wherein R E and R F are each independently selected from hydrogen, -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]- [L 1 (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) R ] S -(L 1 ) s -R J , -[(LW ⁇ NR 24 ), ⁇ ),]- (L 1 ) s [(C(R 2A ) 2 ) r O(C(R 2A ) 2 ) r (L 2 ) s ] s -(L 1 ) s -R J , optionally substituted d_ 8 alkyl, optionally substituted C3-8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocycly
  • each R is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally substituted heterocyclyl;
  • each R H is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or -NR E R F ;
  • each NR R is independently selected, wherein each R is independently selected from the group consisting of hydrogen, -OH, optionally substituted Ci-Cg alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted -0-(Ci-C 8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, or optionally both R together with the nitrogen to which they are attached are an optionally substituted heterocyclyl; each R is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C 3 -C8 cycloalkyl, optionally substituted -0-(Ci-C 8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
  • each R 2F is independently selected from the group consisting hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C 3 -C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
  • each L 2 is independently selected from the group consisting of optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
  • each m independently is 1 or 2;
  • each n independently is 0, 1, 2, 3, 4, 5, or 6;
  • each r independently is 0, 1, 2, 3, 4, 5, or 6;
  • each s independently is 0 or 1 ;
  • each z independently is 1 or 2
  • R 7 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C 3 -Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
  • R 8 is selected from the group consisting of H (hydrogen), -(CH 2 ) utilizatR C , optionally substituted Ci-Cg alkyl, optionally substituted C 3 -Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
  • X is a group consisting of at least one heteroatom, or selected from groups consisting of -OR 10 , -S02-R 10 , where R 10 is R c
  • the active compound having the structure of Formula I has the structure of Formula lib:
  • R 9 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C 3 -C 8 cycloalkyl, substituted Ci-Cg alkyl, substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally R 7 , R 8 and R 9 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring,
  • X is selected from groups consisting of -OR 10 , -S02-R 10 , where R 10 is R c ; and n is 0 or 1.
  • At least one of R 1 , R 10 and X comprises a targeting moiety. In some embodiments, at least one of R 1 , R 10 and X further comprises a linker. In some embodiments, at least one of R 1 , R 10 and X comprises -(CH 2 ) n - where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, at least one of R 1 , R 10 and X comprises - (CH 2 CH 2 0)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • At least one of R 1 , R 10 and X comprises Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu-Lys, Gly- Gly-Arg, or Ala-Ala-Asn-PAB.
  • At least one of R 1 , R 10 and X comprises a peptide, oligosaccharide, -(CH 2 ) lake-, -(CH 2 CH 2 0) n -, Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu-Lys, Gly-Gly-Arg, Ala-Ala-Asn-PAB, or combinations thereof.
  • the targeting moiety is a monoclonal antibody (mAB).
  • the targeting moiety is an antibody fragment, surrogate, or variant.
  • the targeting moiety is a protein ligand.
  • the targeting moiety is a protein scaffold. In some embodiments, the targeting moiety is a peptide. In some embodiments, the targeting moiety is a small molecule ligand. In some embodiments, the linker includes a 4-carbon bridge and at least two sulfur atoms. In some embodiments, the linker includes a fragment selected from the group consisting of:
  • At least one of R 1 , R 10 and X comprises
  • the A-component is the targeting moiety;
  • the E-component is an optionally substituted heteroaryl or an optionally substituted heterocyclyl;
  • L 3 is an optionally substituted Ci-C 6 alkyl, or L 3 is null, when L 3 is null the sulfur is directly connected to the E-component;
  • L 4 is an optionally substituted Ci-C 6 alkyl, or L 4 is null, when L 4 is null the sulfur is directly connected to the E-component.
  • the E-component includes a fragment selected from the group consisting of:
  • L is -(CH 2 )-; and L is -(CH 2 )-. In some embodiments, L is null; and L 4 i iss nnuullll..
  • At least one ofR 1 , R 10 and X comprises:
  • A is the targeting moiety; X is N (nitrogen) or CH; Y is N (nitrogen), or CH; m is 0, 1, or 2; L is a linker, or null; and L 1A is a linker, or null.
  • L is null.
  • At least one of R 1 , R 10 and X comprises, consists of, ists essentially of:
  • L may be optionally substituted Ci-C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • L 5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L 5 is Ci-Cg alkyl.
  • At least one of R 1 , R 10 and X comprises, consists of, or consist essentially of:
  • L may be optionally substituted Ci-Cg alkyl, optionally substituted C 3 -Cg cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • L 5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L 5 is Ci-Cg alkyl.
  • At least one of R 1 , R 10 and X comprises, consists of, or consist essentially of: , wherein A is the targeting moiety, L 5 may be optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted Ci-C 8 alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L 5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L 5 is Ci-Cg alkyl.
  • L 6 may be H, optionally substituted Ci-C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • At least one of R 1 , R 10 and X comprises, consists of, or consist essentially of:
  • L 5 may be optionally substituted Ci-C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted C3-C8 cylcoalkyl annulated to cyclooctyl ring, optionally substituted Ci-C 8 alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • L 5 is an optionally substituted Ci-C 8 alkyl.
  • L 5 is Ci-C 8 alkyl.
  • Some embodiments provide a compound-conjugate having the structure of Formula V:
  • a 1 may be a targeting moiety
  • B 1 is an auxiliary moiety that optionally includes a second targeting moiety, or B 1 is null
  • L 1 includes a group including a N (nitrogen) atom or a group including a 2- to
  • a 1 may be a monoclonal antibody (mAB). In some embodiments, A 1 may be an antibody fragment, surrogate, or variant. In some embodiments, A 1 may be a protein ligand. In some embodiments, A 1 may be a protein scaffold. In some embodiments, A 1 may be a peptide. In some embodiments, A 1 may be RNA or DNA. In some embodiments, A 1 may be a RNA or DNA fragment.
  • mAB monoclonal antibody
  • a 1 may be an antibody fragment, surrogate, or variant.
  • a 1 may be a protein ligand. In some embodiments, A 1 may be a protein scaffold. In some embodiments, A 1 may be a peptide. In some embodiments, A 1 may be RNA or DNA. In some embodiments, A 1 may be a RNA or DNA fragment.
  • a 1 may be a small molecule ligand.
  • B 1 may be a hydrophilic polymer.
  • the hydrophilic polymer may polyethylene glycol (PEG), and the like.
  • B 1 may be a biodegradable polymer.
  • the biodegradable polymer may be unstructured proteins polyamino acids, polypeptides polysaccharides and combinations thereof.
  • B 1 may be a monoclonal antibody (mAB).
  • mAB monoclonal antibody
  • B 1 may be an antibody fragment, surrogate, or variant.
  • B 1 may be a protein ligand.
  • B 1 may be a protein scaffold.
  • B 1 may be a peptide.
  • B 1 may be RNA or DNA.
  • B 1 may be a RNA or
  • B 1 may be a small molecule ligand.
  • D may includes a biologically active compound.
  • D may includes a core from tubulin-binder or tubulin-binder derivative.
  • D include a core from epothilone A, epothilone B, paclitaxel, or derivatives thereof.
  • D includes
  • A is a tubulin binding moiety
  • B is a protease inhibition moiety
  • Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, substituted or cyclic Ci-Cg alkyl, aryl, and substituted aryl, or optionally Ri and R 2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally R 7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring.
  • A may be
  • A may be ; may be N (nitrogen), CH, C-OH, C-OR,
  • L 2 may include a spacer or a multifunctional linker. In some embodiments, L 2 may include a spacer and a multifunctional linker. In some embodiments, L 2 may include a multifunctional linker.
  • each L 2 may be a linker, wherein the linker may be cleavable or non-cleavable under biological conditions. In some embodiments, the linker may be cleavable by an enzyme. In some embodiments, L 2 may include Linker. In some embodiments, L 1 includes a cyclic group including at least one N (nitrogen) atom. In some embodiments, L 1 includes a cyclic group including at least two N (nitrogen) atoms. In some embodiments, L 1 includes a cyclic group including at least one N (nitrogen) atom and a spacer. In some embodiments, L 1 includes a cyclic group including at least two N (nitrogen) atoms and a spacer.
  • the spacer connects to the mAB by an amide bond. In some embodiments, the spacer connects to the mAB through an amine bond.
  • L 1 includes a 2- to 5- carbon bridge and at least one sulfur atom. In some embodiments, L 1 includes a 2- to 5- carbon bridge and at least two sulfur atoms. In some embodiments, L 1 includes a 2- to 5- carbon bridge and a spacer. In some embodiments, L 1 includes a 2- to 5 -carbon bridge, at least two sulfur atoms and a spacer. In some embodiments, L 1 may include one or more sulfurs. In some embodiments, the L 1 may include two or more sulfurs. In some embodiments, the L 1 may include exactly two sulfurs.
  • L 1 may include a 4-carbon bridge and/or a spacer.
  • L 1 include a 4-carbon bridge or a spacer.
  • L 1 may include a 4-carbon bridge and a spacer.
  • L 1 includes a 4-carbon bridge and at least two sulfur atoms.
  • the spacer connects to the mAB by a sulfide bond.
  • the spacer connects to the mAB through a thioether.
  • a 1 comprises at least one modified n-butyl L-a-amino acid.
  • at least one modified L-Lysine residue is from an L-Lysine residue of a peptide before conjugation.
  • At least one nitrogen of L 1 is from an at least one modified n-butyl L-a-amino acid of a peptide before conjugation.
  • a 1 and L 1 together comprise at least one modified L-Lysine residue.
  • the terminal nitrogen of the side chain of an L- Lysine residue of a peptide before conjugation is the at least one N (nitrogen) atom of L 1 .
  • a 1 comprises the -(CH 2 )4- of the side chain of an L-Lysine residue of a peptide before conjugation that provides the at least one N (nitrogen) atom of L 1 .
  • a 1 comprises a modified n-butyl a-amino acid residue.
  • Linker may be a peptide.
  • Linker may include an oligosaccharide.
  • Linker may include chitosan.
  • L 2 may include Linker and - (CH 2 ) reckon- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • L 2 may include Linker and -(CH 2 CH 2 0) n - where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • Linker may include -(CH 2 ) opinion- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • Linker may include -(CH 2 CH 2 0) n - where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • Linker may include Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu- Lay, Gly-Gly-Arg, Ala-Ala-Asn-PAB, or the like.
  • Linker may include any combination of peptide, oligosaccharide, -(CH 2 ) briefly-, -(CH 2 CH 2 0) n -, Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu-Lay, Gly-Gly-Arg, Ala-Ala-Asn-PAB, and the like.
  • the spacer may include a peptide.
  • the spacer may include an oligosaccharide.
  • the spacer may include chitosan.
  • the spacer may include -(CH 2 ) compassion- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • L 1 may include a component including a 4-carbon bridge and -(CH 2 ) admir- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • the spacer may include - (CH 2 CH 2 0) n - where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • L 1 may include a component including a 4-carbon bridge and -(CH 2 CH 2 0) n - where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
  • the spacer may include Val-Cit-PAB, Val-Ala-PAB, Phe- Lys-PAB, Ala-Ala-Asn-PAB, or the like.
  • the spacer may be any combination of peptide, oligosaccharide, -(CH 2 ) seldom-, -(CH 2 CH 2 0) n -, Val-Cit-PAB, Val-Ala- PAB, Phe-Lys-PAB, Ala-Ala-Asn-PAB, and the like.
  • L 1 may include,
  • the compound-conjugates may include one or more components selected from the group consisting of an amino acid, an amino acid residue, an amino acid analog, and a modified amino acid.
  • peptide refers to a structure including one or more components each individually selected from the group consisting of an amino acid, an amino acid residue, an amino acid analog, and a modified amino acid. The components are typically joined to each other through an amide bond.
  • amino acid includes naturally occurring amino acids, a molecule having a nitrogen available for forming an amide bond and a carboxylic acid, a molecule of the general formula NH 2 -CHR-COOH or the residue within a peptide bearing the parent amino acid, where "R” is one of a number of different side chains.
  • R can be a substituent found in naturally occurring amino acids.
  • R can also be a substituent referring to one that is not of the naturally occurring amino acids.
  • amino acid residue refers to the portion of the amino acid which remains after losing a water molecule when it is joined to another amino acid.
  • amino acid analog refers to a structural derivative of an amino acid parent compound that often differs from it by a single element.
  • modified amino acid refers to an amino acid bearing an "R" substituent that does not correspond to one of the twenty genetically coded amino acids.
  • the abbreviations for the genetically encoded L- enantiomeric amino acids are conventional and are as follows:
  • amino acid residues in the compound-conjugate can be replaced with other amino acid residues without significantly deleteriously affecting, and in many cases even enhancing, the activity of the peptides.
  • altered or mutated forms of the active agent-conjugate wherein at least one defined amino acid residue in the structure is substituted with another amino acid residue or derivative and/or analog thereof. It will be recognized that in preferred embodiments, the amino acid substitutions are conservative, i.e., the replacing amino acid residue has physical and chemical properties that are similar to the amino acid residue being replaced.
  • the amino acids can be conveniently classified into two main categories—hydrophilic and hydrophobic—depending primarily on the physical-chemical characteristics of the amino acid side chain. These two main categories can be further classified into subcategories that more distinctly define the characteristics of the amino acid side chains.
  • hydrophilic amino acids can be further subdivided into acidic, basic and polar amino acids.
  • hydrophobic amino acids can be further subdivided into nonpolar and aromatic amino acids.
  • the definitions of the various categories of amino acids are as follows:
  • hydrophilic amino acid refers to an amino acid exhibiting a hydrophobicity of less than zero according to the normalized consensus hydrophobicity scale of Eisenberg et al., 1984, J. Mol. Biol. 179: 125-142. Genetically encoded hydrophilic amino acids include Thr (T), Ser (S), His (H), Glu (E), Asn (N), Gin (Q), Asp (D), Lys (K) and Arg (R).
  • hydrophobic amino acid refers to an amino acid exhibiting a hydrophobicity of greater than zero according to the normalized consensus hydrophobicity scale of Eisenberg, 1984, J. Mol. Biol. 179:1.25-142. Genetically encoded hydrophobic amino acids include Pro (P), He (I), Phe (F), Val (V), Leu (L), Trp (W), Met (M), Ala (A), Gly (G) and Tyr (Y).
  • acidic amino acid refers to a hydrophilic amino acid having a side chain pK value of less than 7. Acidic amino acids typically have negatively charged side chains at physiological pH due to loss of a hydrogen ion. Genetically encoded acidic amino acids include Glu (E) and Asp (D).
  • basic amino acid refers to a hydrophilic amino acid having a side chain pK value of greater than 7.
  • Basic amino acids typically have positively charged side chains at physiological pH due to association with hydronium ion.
  • Genetically encoded basic amino acids include His (H), Arg (R) and Lys (K).
  • polar amino acid refers to a hydrophilic amino acid having a side chain that is uncharged at physiological pH, but which has at least one bond in which the pair of electrons shared in common by two atoms is held more closely by one of the atoms.
  • Genetically encoded polar amino acids include Asn (N), Gin (Q) Ser (S) and Thr (T).
  • nonpolar amino acid refers to a hydrophobic amino acid having a side chain that is uncharged at physiological pH and which has bonds in which the pair of electrons shared in common by two atoms is generally held equally by each of the two atoms (i.e., the side chain is not polar). Genetically encoded nonpolar amino acids include Leu (L), Val (V), He (I), Met (M), Gly (G) and Ala (A).
  • aromatic amino acid refers to a hydrophobic amino acid with a side chain having at least one aromatic or heteroaromatic ring.
  • the aromatic or heteroaromatic ring may contain one or more substituents such as— OH,— SH, — CN,— F,—CI,—Br,—I,— N0 2 ,—NO,— NH 2 ,— NHR,— NRR,— C(0)R,— C(0)OH, — C(0)OR, — C(0)NH 2 , — C(0)NHR, — C(0)NRR and the like where each R is independently (Ci - C 6 ) alkyl, substituted (Ci - C 6 ) alkyl, (Ci - C 6 ) alkenyl, substituted (Ci - C 6 ) alkenyl, (Ci - C 6 ) alkynyl, substituted (Ci - C 6 ) alkynyl, (C 5 - C 20 ) aryl, substituted (C 5 - C 2 o) aryl, (C 6 - C 26 ) alkaryl, substituted (C 6 - C 6
  • aliphatic amino acid refers to a hydrophobic amino acid having an aliphatic hydrocarbon side chain. Genetically encoded aliphatic amino acids include Ala (A), Val (V), Leu (L) and He (I).
  • Cys (C) is unusual in that it can form disulfide bridges with other Cys (C) residues or other sulfanyl-containing amino acids.
  • the ability of Cys (C) residues (and other amino acids with— SH containing side chains) to exist in a peptide in either the reduced free— SH or oxidized disulfide -bridged form affects whether Cys (C) residues contribute net hydrophobic or hydrophilic character to a peptide.
  • Cys (C) exhibits a hydrophobicity of 0.29 according to the normalized consensus scale of Eisenberg (Eisenberg, 1984, supra), it is to be understood that for purposes of the preferred embodiments Cys (C) is categorized as a polar hydrophilic amino acid, notwithstanding the general classifications defined above.
  • targeting moiety refers to a structure that binds or associates with a biological moiety or fragment thereof.
  • the targeting moiety may be a monoclonal antibody (mAB). In some embodiments, the targeting moiety may be an antibody fragment, surrogate, or variant. In some embodiments, the targeting moiety may be a protein ligand. In some embodiments, the targeting moiety may be a protein scaffold. In some embodiments, the targeting moiety may be a peptide. In some embodiments, the targeting moiety may be RNA or DNA. In some embodiments, the targeting moiety may be a RNA or DNA fragment. In some embodiments, the targeting moiety may be a small molecule ligand.
  • mAB monoclonal antibody
  • the targeting moiety may be an antibody fragment, surrogate, or variant.
  • the targeting moiety may be a protein ligand. In some embodiments, the targeting moiety may be a protein scaffold. In some embodiments, the targeting moiety may be a peptide. In some embodiments, the targeting moiety may be RNA or DNA. In some embodiments, the targeting moiety may be a RNA or
  • the targeting moiety may be an antibody fragment described in Janthur et al., "Drug Conjugates Such as Antibody Drug Conjugates (ADCs), Immunotoxins and Immunoliposomes Challenge Daily Clinical Practice," Int. J. Mol. Sci. 2012, 13, 16020-16045, the disclosure of which is incorporated herein by reference in its entirety.
  • the targeting moiety may be an antibody fragment described in Trail, PA, "Antibody Drug Conjugates as Cancer Therapeutics," Antibodies 2013, 2, 113- 129, the disclosure of which is incorporated herein by reference in its entirety.
  • the targeting moiety may be HuM195-Ac-225, HuM195-Bi-213, Anyara (naptumomab estafenatox; ABR-217620), AS1409, Zevalin (ibritumomab tiuxetan), BIIB015, BT-062, Neuradiab, CDX-1307, CR011-vcMMAE, Trastuzumab-DMl (R3502), Bexxar (tositumomab), IMGN242, IMGN388, IMGN901, 131 I- labetuzumab, IMMU-102 ( 90 Y-epratuzumab), IMMU-107 ( 90 Y-clivatuzumab tetraxetan), MDX-1203, CAT-8015, EMD 273063 (hul4.18-IL2), Tucotuzumab celmoleukin (EMD 273066; h
  • the targeting moiety may comprise, consist of, or consist essentially of the antibody portion of HuM195-Ac-225, HuM195-Bi-213, Anyara (naptumomab estafenatox; ABR-217620), AS 1409, Zevalin (ibritumomab tiuxetan), BUBO 15, BT-062, Neuradiab, CDX-1307, CR011-vcMMAE, Trastuzumab-DMl (R3502), Bexxar (tositumomab), IMGN242, IMGN388, IMGN901, 131 I-labetuzumab, IMMU-102 ( 90 Y- epratuzumab), IMMU-107 ( 90 Y-clivatuzumab tetraxetan), MDX-1203, CAT-8015, EMD 273063 (hul4.18-IL2), Tucotuzumab celmoleukin (
  • the targeting moiety may be Brentuximab vedotin, Trastuzumab emtansine, Inotuzumab ozogamicin, Lorvotuzumab mertansine, Glembatumumab vedotin, SAR3419, Moxetumomab pasudotox, Moxetumomab pasudotox, AGS-16M8F, AGS-16M8F, BIIB-015, BT-062, IMGN-388, or IMGN-388.
  • the targeting moiety may comprise, consist of, or consist essentially of the antibody portion of Brentuximab vedotin, Trastuzumab emtansine, Inotuzumab ozogamicin, Lorvotuzumab mertansine, Glembatumumab vedotin, SAR3419, Moxetumomab pasudotox, Moxetumomab pasudotox, AGS-16M8F, AGS-16M8F, BIIB-015, BT-062, IMGN-388, or IMGN-388.
  • the targeting moiety may comprise, consist of, or consist essentially of Brentuximab, Inotuzumab, Gemtuzumab, Milatuzumab, Trastuzumab, Glembatumomab, Lorvotuzumab, or Labestuzumab.
  • linker refers to a moiety that connects two or more components to each other.
  • the linker may be a linker disclosed in Janthur et al., "Drug Conjugates Such as Antibody Drug Conjugates (ADCs), Immunotoxins and Immunoliposomes Challenge Daily Clinical Practice," Int. J. Mol. Sci. 2012, 13, 16020- 16045.
  • the linker may be a linker disclosed in Trail, PA, "Antibody Drug Conjugates as Cancer Therapeutics," Antibodies 2013, 2, 113-129.
  • the linker may be a linker disclosed in US Patent No.: 7,829, 531.
  • the linker may comprise, consist of, or consist essentially of the linker portion of HuM195-Ac-225, HuM195-Bi-213, Anyara (naptumomab estafenatox; ABR-217620), AS 1409, Zevalin (ibritumomab tiuxetan), BUBO 15, BT-062, Neuradiab, CDX-1307, CR011-vcMMAE, Trastuzumab-DMl (R3502), Bexxar (tositumomab), IMGN242, IMGN388, IMGN901, 131 I-labetuzumab, IMMU-102 ( 90 Y- epratuzumab), IMMU-107 ( 90 Y-clivatuzumab tetraxetan), MDX-1203, CAT-8015, EMD 273063 (hul4.18-IL2), Tucotuzumab celmol
  • the linker may comprise, consist of, or consist essentially of the linker portion of Brentuximab vedotin, Trastuzumab emtansine, Inotuzumab ozogamicin, Lorvotuzumab mertansine, Glembatumumab vedotin, SAR3419, Moxetumomab pasudotox, Moxetumomab pasudotox, AGS-16M8F, AGS-16M8F, BIIB-015, BT-062, IMGN-388, or IMGN-388.
  • the linker may comprise, consist of, or consist essentially of Valine-citrulline residue, hydrazine, 4-mercaptobutanoyl, 4-(N- succinimidomethyl)cyclohexanecarbonyl (SMCC), Maleimidocaproyl, Phenylalaninelysine, 6-(3-(thio)propanamido)hexanoyl, 3-mercaptopropanoyl, 4-mercaptopentanoyl, or lysine residue.
  • SMCC succinimidomethylcyclohexanecarbonyl
  • the linker may comprise, consist of, or consist essentially of:
  • L 5 may be optionally substituted Ci-C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • L 5 is an optionally substituted Ci-Cg alkyl.
  • L 5 is Ci-Cg alkyl.
  • the linker may comprise, consist of, or consist essentially of:
  • L may be optionally substituted Ci-Cg alkyl, optionally substituted C 3 -Cg cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • L 5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L 5 is Ci-Cg alkyl.
  • the linker may comprise, consist of, or consist essentially of:
  • L 5 is an optionally substituted
  • L 5 is Ci-Cg alkyl.
  • L 6 may be H, optionally substituted Ci-
  • Cg alkyl optionally substituted C 3 -Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • the linker may comprise, consist of, or consist essentially of:
  • L 5 may be optionally substituted Ci-Cg alkyl, optionally substituted C 3 -Cg cycloalkyl, optionally substituted C3-C8 cylcoalkyl annulated to cyclooctyl ring, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
  • L 5 is an optionally substituted Ci-Cg alkyl.
  • L 5 is Ci-Cg alkyl.
  • the linker may comprise, consist of, or consist essentially of:
  • amino acids having side chains exhibiting two or more physical-chemical properties can be included in multiple categories.
  • amino acid side chains having aromatic moieties that are further substituted with polar substituents, such as Tyr (Y) may exhibit both aromatic hydrophobic properties and polar or hydrophilic properties, and can therefore be included in both the aromatic and polar categories.
  • polar substituents such as Tyr (Y)
  • the amino acid substitutions need not be, and in certain embodiments preferably are not, restricted to the genetically encoded amino acids.
  • the active agent-conjugate may contain genetically non-encoded amino acids.
  • amino acid residues in the active agent-conjugate may be substituted with naturally occurring non- encoded amino acids and synthetic amino acids.
  • Certain commonly encountered amino acids which provide useful substitutions for the active agent-conjugates include, but are not limited to, ⁇ -alanine ( ⁇ -Ala) and other omega-amino acids such as 3-aminopropionic acid, 2,3-diaminopropionic acid (Dpr), 4-aminobutyric acid and so forth; a-aminoisobutyric acid (Aib); ⁇ -aminohexanoic acid (Aha); ⁇ -aminovaleric acid (Ava); N-methylglycine or sarcosine (MeGly); ornithine (Orn); citrulline (Cit); t-butylalanine (t-BuA); t-butylglycine (t-BuG); N-methylisoleucine (Melle); phenylglycine (Phg); cyclohexylalanine (Cha); norleucine (Nle); naphthylalanine (Nal); 4-
  • Aromatic F Y, W Phg, Nal, Thi, Tic, Phe (4-Cl), Phe (2-F),
  • the amino acids of the compound-conjugate will be substituted with L-enantiomeric amino acids, the substitutions are not limited to L- enantiomeric amino acids.
  • the peptides may advantageously be composed of at least one D-enantiomeric amino acid. Peptides containing such D-amino acids are thought to be more stable to degradation in the oral cavity, gut or serum than are peptides composed exclusively of L-amino acids.
  • Examples of compound-conjugates include, but are not limited to, the following general compounds:
  • R may be H (hydrogen), Ci-Cg alkyl, substituted or cyclic Ci-Cg alkyl
  • Examples of compounds include, but are not limited to, the following general compounds:
  • compound-conjugates include, but are not limited to, the following general compounds:
  • R may be H (hydrogen), Ci-C 8 alkyl, substituted or cyclic Ci-C 8 alkyl, and the like
  • Examples of compounds include, but are not limited to, the following compound and general compounds:
  • the compounds disclosed herein are used in pharmaceutical compositions.
  • the compounds can be used, for example, in pharmaceutical compositions comprising a pharmaceutically acceptable carrier prepared for storage and subsequent administration.
  • embodiments relate to a pharmaceutically effective amount of the products and compounds disclosed above in a pharmaceutically acceptable carrier or diluent.
  • Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A.R. Gennaro edit. 1985), which is incorporated herein by reference in its entirety.
  • Preservatives, stabilizers, dyes and even flavoring agents can be provided in the pharmaceutical composition.
  • sodium benzoate, ascorbic acid and esters of p- hydroxybenzoic acid can be added as preservatives.
  • antioxidants and suspending agents can be used.
  • compositions can be formulated and used as tablets, capsules, or elixirs for oral administration; suppositories for rectal administration; sterile solutions, suspensions for injectable administration; patches for transdermal administration, and sub- dermal deposits and the like.
  • injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. Suitable excipients are, for example, water, saline, dextrose, mannitol, lactose, lecithin, albumin, sodium glutamate, cysteine hydrochloride, and the like.
  • the injectable pharmaceutical compositions may contain minor amounts of nontoxic auxiliary substances, such as wetting agents, pH buffering agents, and the like. If desired, absorption enhancing preparations (for example, liposomes), can be utilized.
  • compositions for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds can be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or other organic oils such as soybean, grapefruit or almond oils, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes.
  • Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran.
  • the suspension may also contain suitable stabilizers or agents that increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
  • compositions for oral use can be obtained by combining the active compounds with solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores.
  • suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP).
  • PVP polyvinylpyrrolidone
  • disintegrating agents can be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
  • Dragee cores are provided with suitable coatings.
  • suitable coatings for this purpose, concentrated sugar solutions can be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs or pigments can be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
  • concentrated sugar solutions can be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs or pigments can be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
  • ком ⁇ онентs to formulate the compounds of Formulae I and II as an anti-cancer agent, known surface active agents, excipients, smoothing agents, suspension agents and pharmaceutically acceptable film-forming substances and coating assistants, and the like can be used.
  • alcohols, esters, sulfated aliphatic alcohols, and the like can be used as surface active agents; sucrose, glucose, lactose, starch, crystallized cellulose, mannitol, light anhydrous silicate, magnesium aluminate, magnesium methasilicate aluminate, synthetic aluminum silicate, calcium carbonate, sodium acid carbonate, calcium hydrogen phosphate, calcium carboxymethyl cellulose, and the like can be used as excipients; magnesium stearate, talc, hardened oil and the like can be used as smoothing agents; coconut oil, olive oil, sesame oil, peanut oil, soya can be used as suspension agents or lubricants; cellulose acetate phthalate as a derivative of a carbohydrate such
  • the compounds of Formulae I and II or compositions including compounds of Formulae I and II can be administered by either oral or non-oral pathways.
  • it can be administered in capsule, tablet, granule, spray, syrup, or other such form.
  • it can be administered as an aqueous suspension, an oily preparation or the like or as a drip, suppository, salve, ointment or the like, when administered via injection, subcutaneously, intraperitoneally, intravenously, intramuscularly, or the like.
  • the anti-cancer agent can be mixed with additional substances to enhance their effectiveness.
  • the disclosed compounds and the disclosed pharmaceutical compositions are administered by a particular method as an anti-cancer, or anti-inflammatory.
  • Such methods include, among others, (a) administration though oral pathways, which administration includes administration in capsule, tablet, granule, spray, syrup, or other such forms; (b) administration through non-oral pathways, which administration includes administration as an aqueous suspension, an oily preparation or the like or as a drip, suppository, salve, ointment or the like; administration via injection, subcutaneously, intraperitoneally, intravenously, intramuscularly, intradermally, or the like; as well as (c) administration topically, (d) administration rectally, or (e) administration vaginally, as deemed appropriate by those of skill in the art for bringing the compound of the present embodiment into contact with living tissue; and (f) administration via controlled released formulations, depot formulations, and infusion pump delivery.
  • compositions that include the described compounds required as a dose will depend on the route of administration, the type of animal, including human, being treated, and the physical characteristics of the specific animal under consideration.
  • the dose can be tailored to achieve a desired effect, but will depend on such factors as weight, diet, concurrent medication and other factors which those skilled in the medical arts will recognize.
  • a compound represented by Formulae I and II can be administered to a patient in need of an anti-cancer agent, until the need is effectively reduced or preferably removed.
  • the products or compositions can be used alone or in combination with one another, or in combination with other therapeutic or diagnostic agents. These products can be utilized in vivo, ordinarily in a mammal, preferably in a human, or in vitro. In employing them in vivo, the products or compositions can be administered to the mammal in a variety of ways, including parenterally, intravenously, subcutaneously, intramuscularly, colonically, rectally, vaginally, nasally or intraperitoneally, employing a variety of dosage forms. Such methods may also be applied to testing chemical activity in vivo.
  • the useful in vivo dosage to be administered and the particular mode of administration will vary depending upon the age, weight and mammalian species treated, the particular compounds employed, and the specific use for which these compounds are employed.
  • the determination of effective dosage levels can be accomplished by one skilled in the art using routine pharmacological methods. Typically, human clinical applications of products are commenced at lower dosage levels, with dosage level being increased until the desired effect is achieved. Alternatively, acceptable in vitro studies can be used to establish useful doses and routes of administration of the compositions identified by the present methods using established pharmacological methods.
  • dosages In non-human animal studies, applications of potential products are commenced at higher dosage levels, with dosage being decreased until the desired effect is no longer achieved or adverse side effects disappear.
  • the dosage may range broadly, depending upon the desired affects and the therapeutic indication. Typically, dosages can be between about 10 mg/kg and 100 mg/kg body weight, preferably between about 100 mg/kg and 10 mg/kg body weight. Alternatively dosages can be based and calculated upon the surface area of the patient, as understood by those of skill in the art. Administration is preferably oral on a daily or twice daily basis.
  • the exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. See for example, Fingl et al. , in The Pharmacological Basis of Therapeutics, 1975, which is incorporated herein by reference in its entirety. It should be noted that the attending physician would know how to and when to terminate, interrupt, or adjust administration due to toxicity, or to organ dysfunctions. Conversely, the attending physician would also know to adjust treatment to higher levels if the clinical response were not adequate (precluding toxicity).
  • the magnitude of an administrated dose in the management of the disorder of interest will vary with the severity of the condition to be treated and to the route of administration. The severity of the condition may, for example, be evaluated, in part, by standard prognostic evaluation methods. Further, the dose and perhaps dose frequency, will also vary according to the age, body weight, and response of the individual patient. A program comparable to that discussed above can be used in veterinary medicine.
  • Suitable administration routes may include oral, rectal, transdermal, vaginal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.
  • the agents of the embodiment can be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiological saline buffer.
  • physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiological saline buffer.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art.
  • Use of pharmaceutically acceptable carriers to formulate the compounds herein disclosed for the practice of the embodiment into dosages suitable for systemic administration is within the scope of the embodiment. With proper choice of carrier and suitable manufacturing practice, the compositions disclosed herein, in particular, those formulated as solutions, can be administered parenterally, such as by intravenous injection.
  • the compounds can be formulated readily using pharmaceutically acceptable carriers well known in the art into dosages suitable for oral administration.
  • Such carriers enable the compounds of the embodiment to be formulated as tablets, pills, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated.
  • Agents intended to be administered intracellularly can be administered using techniques well known to those of ordinary skill in the art. For example, such agents can be encapsulated into liposomes, then administered as described above. All molecules present in an aqueous solution at the time of liposome formation are incorporated into the aqueous interior. The liposomal contents are both protected from the external micro- environment and, because liposomes fuse with cell membranes, are efficiently delivered into the cell cytoplasm. Additionally, due to their hydrophobicity, small organic molecules can be directly administered intracellularly.
  • these pharmaceutical compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically.
  • suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically.
  • the preparations formulated for oral administration can be in the form of tablets, dragees, capsules, or solutions.
  • the pharmaceutical compositions can be manufactured in a manner that is itself known, for example, by means of conventional mixing, dissolving, granulating, dragee-making, levitating, emulsifying, encapsulating, entrapping, or lyophilizing processes.
  • Compounds disclosed herein can be evaluated for efficacy and toxicity using known methods.
  • the toxicology of a particular compound, or of a subset of the compounds, sharing certain chemical moieties can be established by determining in vitro toxicity towards a cell line, such as a mammalian, and preferably human, cell line. The results of such studies are often predictive of toxicity in animals, such as mammals, or more specifically, humans.
  • the toxicity of particular compounds in an animal model such as mice, rats, rabbits, dogs or monkeys, can be determined using known methods.
  • the efficacy of a particular compound can be established using several art recognized methods, such as in vitro methods, animal models, or human clinical trials.
  • needle is not an absolute term and merely implies that the patient can benefit from the treatment of the anti-cancer agent in use.
  • patient what is meant is an organism that can benefit by the use of an anticancer agent.
  • “Therapeutically effective amount,” “pharmaceutically effective amount,” or similar term means that amount of drug or pharmaceutical agent that will result in a biological or medical response of a cell, tissue, system, animal, or human that is being sought. In a preferred embodiment, the medical response is one sought by a researcher, veterinarian, medical doctor, or other clinician.
  • a described compound preferably a compound having any one of Formulas I and II, including those as described herein, is considered an effective anti-cancer agent if the compound can influence 10% of the cancer cells, for example.
  • the compound is effective if it can influence 10 to 50% of the cancer cells.
  • the compound is effective if it can influence 50-80% of the cancer cells.
  • the compound is effective if it can influence 80-95% of the cancer cells.
  • the compound is effective if it can influence 95-99% of the cancer cells.
  • "Influence" is defined by the mechanism of action for each compound.
  • Conjugation method B Conjugation on Lys residues via reductive alkylation with an dialdehyde
  • Conjugation method D Conjugation on two Cys side chains by forming a cyclic structure
  • Method 1-1 Linker and Drug connected via a carbamate bond. The following general procedures were employed:
  • Method 1-3 Active molecule containing a carboxylic acid moiety connected to an alkoxyamino linker via formation of hydoxamate (General procedure A or B), followed by removal of protective groups.
  • Step 3 Introducing the final functional groups prior to conjugation
  • the carboxylic acid can be activated using a variety of methods to afford an activated form.
  • the carboxylic acid can be activated using the following methods: A) Tetrahedron 61 (2005) 10827-10852; B) Beckwith, A. L. J. In The Chemistry of
  • amino acid sulfonamide derivatives 11, 15, 17, 19 were synthesized according to previously reported procedure (ARKIVOC 2004 (xii) 14-22) using Boc protected amino acid and cyclopropyl/methyl sulfonamide, followed by removal of Boc
  • Compound 27 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between compound 21 and amine 25, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 27 as a white powder after lyophilization. MS m/z Calcd. for C 3 6H 5 9N 5 0 8 S 721.4, Found 722.5 ([M+H] + ).
  • Compound 30 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between ⁇ -Cl-N-Boc-Ala-OH (compound 28) and amine 27, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 30 as a white powder after lyophilization. MS m/z Calcd for C 3 H 63 CIN 6 O 9 S 826.4, Found 827.5 ([M+H] + ).
  • amino acid sulfonamide derivatives 33 and 36 were synthesized according to previously reported procedure (WO 2007146695) using Boc protected amino acid and cyclopropyl/methyl sulfonamide, followed by removal of Boc (General procedure C)
  • Compound 35 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 10) and amine 33, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 35 as a white powder after lyophilization. MS m/z Calcd for
  • the compound 45 was synthesized according to the same procedures as described for the synthesis of compound 44. The final compound was purified by reverse phase HPLC to give compound 45 as a white powder after lyophilization. MS m/z Calcd for
  • Example III -4 Other compounds synthesized using the same procedures as described for the synthesis of compound 49
  • the intermediate 136 was synthesized using the general procedures described above as following (0.1 mmol scale): HATU mediated amide bond formation
  • the compound 138 was synthesized employing the same sequence as described for the preparation of compound 137. (compound 139 as a starting material). It was obtained as a white powder after RP-HPLC purification and lyophilization. MS m/z Calcd for
  • Compound 56 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Me 2 -Val-Val-Dil-Dap-LeuOH (compound 49) and THP-0-NH 2 , followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 56 as a white powder after lyophilization. MS m/z
  • Dimethyl Auristatin F was synthesized from compound 10 and NH 2 -Phe-
  • Compound 60 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 50 and THP-0-NH 2 , followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 47 as a white powder after lyophilization. MS m/z Calcd for C 3 9H 72 N 6 0 8 752.5,
  • Compound 61 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 52 and THP-0-NH 2 , followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 61 as a white powder after lyophilization. MS m/z Calcd for C 4 iH 78 N 6 0 9 798.5,
  • Compound 84 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Auristatin F and compound 66, followed by removal of Fmoc (General procedure
  • Compound 98 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 4 and Fmoc-A-PAB-PNP, followed by removal of Fmoc (General procedure D), and amide formation with acid 87 using HATU (General procedure A, 3eq of acid 87 and 1 eq of HATU were used). The final compound was purified by reverse phase HPLC to give compound 98 as a white powder after lyophilization. MS m/z Calcd for C 61 H 94 N 8 O 17 S 1242.7, Found 1243.8 ([M+H] + ).
  • Compound 102 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 16 and Fmoc-A-PAB-PNP, followed by removal of Fmoc (General procedure D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 102 as a white powder after lyophilization. MS m/z Calcd for C 55 H 9 oN 8 Oi 5 S 1134.6, Found 1135.6 ([M+H] + ).
  • Compound 103 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 16 and Fmoc-A-PAB-PNP, followed by removal of Fmoc (General procedure D), and amide formation with acid 87 using HATU (General procedure A, 3 eq of acid 87 and 1 eq of HATU were used). The final compound was purified by reverse phase HPLC to give compound 103 as a white powder after lyophilization. MS m/z Calcd for CssHgeNgOnS 1208.7, Found 1209.8 ([M+H] + ).
  • Compound 104 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 42 and compound 66, followed by removal of Fmoc (General procedure D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 104 as a white powder after lyophilization. MS m/z Calcd for C71H115N13O19S 1485.8, Found 1486.9 ([M+H] + ).
  • Compound 114 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between compound 113 and methyl isonipecotate, followed by saponification to remove methyl group from ester (General procedure F). The final compound was purified by reverse phase HPLC to give compound 114 as a white powder after lyophilization. MS m/z Calcd for CsiHssNyOisS 1033.6, Found 1034.7 ([M+H] + ).
  • Compound 115 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 113 and compound 67, followed by removal of Fmoc (General procedure D), HATU mediated amidation reaction with acid 116 (General procedure A), and saponification to remove methyl group from ester (General procedure F). The final compound was purified by reverse phase HPLC to give compound 115 as a white powder after lyophilization. MS m/z Calcd for CesHioo ioOnS 1324.7, Found 1325.9 ([M+H] + ).
  • Compound 101 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 13 and FmocVC-PAB-PNP, followed by removal of Fmoc (General procedure D), and amidation reaction with 6-maleimidohexanoic acid (General procedure A). The final compound was purified by reverse phase HPLC to give compound 101 as a white powder after lyophilization. MS m/z Calcd for C71H108N12O17S 1432.8, Found 1433.9 ([M+H] + ).
  • Example X-2 Converting an existing amino group to maleimide directly using N-methoxycarbonylmaleimide
  • HPLC Hydrophilic Interaction Chromatography-HPLC
  • the average DAR drug antibody ratio was calculated by UV absorption and/or MS spectroscopy.
  • the cell lines used were SK-BR-3 human breast adenocarcinoma (HER2 triple positive), HCC1954 human Ductal Carcinoma (HER2 triple positive), MCF7 human breast adenocarcinoma (HER2 normal), and MDA-MB-468 human breast adenocarcinoma
  • SK-BR-3 cells were grown in McCoy's 5 A medium (Caisson Labs, North Logan, UT) supplemented with 10% fetal bovine serum.
  • HCC1954 cells were grown in RPMI-1640 medium (Caisson Labs, North Logan, UT) supplemented with 10% fetal bovine serum.
  • MCF7 and MDA-MB-468 cells were grown in DMEM/F12 medium (Caisson Labs, North Logan, UT) supplemented with 10% fetal bovine serum.
  • SK-BR-3, MCF7, and MDA-MB-468 cells were plated in 96-well plates at approximately 7,500 cells/well, and HCC1954 cells were plated in 96-well plates at approximately 20,000 cells/well. Compounds or the antibody-drug conjugates were added in duplicates in the same day. After 72 hour incubation at 37°C, CellTiter-Glo (Promega, Madison, WI) were added and cell viability was determined as describe by the manufacture's protocol. The percent viability was determined as following:
  • % Viability Average Luminescence Value of the duplicates (treated wells) /

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Abstract

In certain aspects, compounds and uses thereof are provided. In certain aspects, compound-conjugates and uses thereof are provided.

Description

DRUG-CONJUGATES, CONJUGATION METHODS, AND USES THEREOF
BACKGROUND
[0001] Cytotoxic agents can provide therapeutic benefits in the treatment of various conditions, including various cancers. Accordingly, it is desirable to provide cytotoxic agents with therapeutically useful properties, for example, as chemotherapies in cancer treatments.
[0002] Clinical uses of cytotoxic agents as chemotherapies usually develop drug resistances, and thus, drop their therapeutic efficacies. Accordingly, it is desirable to provide cytotoxic agents with improved drug resistance profiles. One possibility is to design cytotoxic compounds with efflux pump resistances. Another possibility is to design cytotoxic compounds potentially act on more than one targets.
[0003] Tubulins are a class of targets for anti-mitotic agents as chemotherapies alone or in combination with other chemotherapies or as active agent-conjugates. Examples of Tubulin-B hidin Agents include, but are not limited to, the following compounds:
Figure imgf000002_0001
Maytansine
Figure imgf000003_0001
Hemiasterlin
Figure imgf000003_0002
HTI-286
[0004] Many enzymes, for example, proteasome, MMAP, FAP and uPA, are considered as cancer therapy targets due to their involvements in cancer proliferations and metastases. Examples of Proteasome inhibitors include, but are not limited to, the following compounds:
Figure imgf000004_0001
Bortezomib CEP-18770 Salinosporamide A
Figure imgf000004_0002
Example of FAP inhibitors, not limited to:
Figure imgf000004_0003
Examples of MMP Inhibitors disclosed in, not limited to:
[0005] Compounds disclosed in Bioorganic & Medicinal Chemistry 15 (2007) 2268.
[0006] Compounds disclosed in Cancer Metastasis Rev (2006) 25: 115-136. SUMMARY
[0007] Some embodiments provide compounds, methods of preparing compounds, and uses thereof.
[0008] Some embodiments provide compound-conjugates, methods of preparing compound-conjugates, and uses thereof.
[0009] Some embodiments provide a compound having the structure of Formula
Figure imgf000005_0001
I
[0010] Some embodiments provide a compound having the structure of Formula la:
Figure imgf000005_0002
(la)
[0011] or a pharmaceutically acceptable salt thereof,
[0012] wherein
[0013] B is a moiety might have contribution to enzyme inhibition or efflux pump resistance;
[0014] R1-R.8 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0015] Y is CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR, where R is Ci-Cg alkyl or substituted Ci-Cg alkyl. [0016] In some embodiments, B may be CN, CHO, CH2OH, CH2F, CH2CN, CH2N3, COOH, CO-N(R)OR, CO-N(R)CO-R, CO-CO-NHR, CO-N(R)-S02R, (CH2)pCOOH, (CH2)p-CH(OH)-COOH, CO-(CH2)p-COOH, CH=CH-COOH, CO-CH=CH- COOH, CH=CH-CONHOH, CH=CH-CONH-S02R, CO-CH=CH-CONHOH, B(OH)2, (CH2)p-B(OH)2, PO(OH)2, or (CH2)p-PO(OH)2, -R-COOH, -R-CO-N(R)OR, -R-CO-NHR, - R-CO-N(R)-S02R, where each occurrence of R is independently selected from H (hydrogen), Ci-Cg alkyl, C3-C8 cycloalkyl, substituted Ci-C8 alkyl, substituted C3-C8 cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and NRERF, and p is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
[0017] In some embodiments, the compound having the structure of Formula I has the structure of F
Figure imgf000006_0001
[0018] or a pharmaceutically acceptable salt thereof,
[0019] B is a moiety might have contribution to enzyme inhibition or efflux pump resistance;
[0020] Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0021] Z is -F, -SR, -N3, -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-C8 alkyl or substituted Ci-C8 alkyl.
[0022] In some embodiments, B may be CN, CHO, CH2OH, CH2F, CH2CN, CH2N3, COOH, CO-NHOH, CO-CO-NHR, CO-NH-S02R, (CH2)nCOOH, (CH2)n-CH(OH)- COOH, CO-(CH2)n-COOH, CH=CH-COOH, CO-CH=CH-COOH, CH=CH-CONHOH, CO- CH=CH-CONHOH, B(OH)2, (CH2)n-B(OH)2, PO(OH)2, or (CH2)n-PO(OH)2, where R = C Cg alkyl or substituted Ci-Cg alkyl, and n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
[0023] Some embodiments provide a compound having the structure of Formula
Ila:
Figure imgf000007_0001
[0024] or a pharmaceutically acceptable salt thereof,
[0025] wherein X is OR10, selected from, but not limited to, a group consisting of at least one hetero atom:
Figure imgf000007_0002
(IIa-1)
[0026] wherein, X is S02R10, selected from, but not limited to, a group consisting of at least one hetero atom:
Figure imgf000007_0003
(IIa-2)
[0027] R1-R10 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally and respectively R7, Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0028] X is a group consisting of at least one heteroatom;
[0029] Y is CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR, where R is Ci-Cg alkyl or substituted Ci-Cg alkyl.
[0030] In some embodiments, the dual active compound having the structure of Formula I has the structure of Formula lib:
Figure imgf000008_0001
[0031] or a pharmaceutically acceptable salt thereof,
[0032] wherein, n is 0 or 1; X is OR10, selected from, but not limited to, a group consisting of at least one hetero atom:
Figure imgf000008_0002
(IIb-1)
[0033] wherein, n is 0 or 1; X is S02R10, selected from, but not limited to, a group consisting of at least one hetero atom:
Figure imgf000008_0003
(IIb-2)
[0034] R1-R10 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally and respectively R7, Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0035] X is a group of at least one heteroatom;
[0036] Z is -F, -SR, -N3, -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-Cg alkyl or substituted Ci-Cg alkyl.
[0037] Also provided herein are the compounds described above conjugated to a targeting moiety with a linker. Also provided herein are the compounds described above with a linker.
[0038] Some embodiments provide a compound having the structure of Formula
IV: R3 R30 u O R6 O R8
R2 O R4 R5 R7
(IV)
or a pharmaceutically acceptable salt thereof,
wherein:
are each independently selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted Ci-Cg alkoxy, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl, or optionally R1 and R2 together with the nitrogen to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R1 and R3 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R7 and R8 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7- membered ring, or optionally R1 is R1A or R1B;
R1A comprises a targeting moiety;
R1B is -L1(CH2)nRc, -L10(CH2)nRc or -(CH2)nRc;
R is Ci-Cg alkyl, C3-Cg cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R , or optionally R comprises a targeting moiety;
each RD is independently selected from the group consisting of -OH, -N3, halo, cyano, nitro, -(CH2)nNRERF, -(CH2)nC(=0)NRERF, — 0(CH2)nNRERF, -0(CH2)nC(=0)NRERF, -0(CH2)mOC(=0)NRERF, -NRGC(=0)RH, -NRGS(0)zRH, -0(CH2)mO(CH2)mRJ, -0(CH2)nC(=0)RJ, -0(CH2)nRJ, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, and optionally substituted -0-(d-C8 alkyl);
each NRERF is independently selected, wherein RE and RF are each independently selected from hydrogen, -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]- [L1(C(R2A)2)r(NR2A)s(C(R2A)2)r]s-(L1)s-RJ, -[(i MQR^ NR^MQR2^),.]- (L1)s[(C(R2A)2)rO(C(R2A)2)r(L2)s]s-(L1)s-RJ, optionally substituted C1-8 alkyl, optionally substituted C3_8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl; each R is independently hydrogen, optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally substituted heterocyclyl;
each RH is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or -NRERF;
each RJ is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)„OR2B, -0(CH2)„OR2B, — (CH2)nNR2BR2B, -C(R2A)2NR2BR2B, -(CH2)nC(=0)OR2B, and -C(=0)NHR2B;
each R2A is independently selected, wherein R2A is selected from the group consisting of hydrogen, halo, -OH, optionally substituted Ci-Cg alkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)nOR2B, -(CH2)nNR2CR2C, -C(=0)OR2B, -C(=0)NR2CR2C, or optionally two geminal R2A and the carbon to which they are attached are together an optionally substituted three- to six-membered carbocyclic ring;
each R2B is independently selected from the group consisting of hydrogen, -OH, -(CH2)nC(=0)OH, -C(=0)(C(R2D)2)nL3R2E, optionally substituted C C8 alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each NR R is independently selected, wherein each R is independently selected from the group consisting of hydrogen, -OH, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, or optionally both R together with the nitrogen to which they are attached are an optionally substituted heterocyclyl;
each R2D is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl; each R is independently selected from the group consisting of optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, and -(CH2)nC(=0)OR2F;
each R2F is independently selected from the group consisting hydrogen, optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L1 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0- -C(=0)NR2A- -S(=0)NR2A- -S(=0)2NR2A- -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each L2 is independently selected from the group consisting of optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L3 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0- -C(=0)NR2A- -S(=0)NR2A-, -S(=0)2NR2A-, -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each m independently is 1 or 2;
each n independently is 0, 1, 2, 3, 4, 5, or 6;
each r independently is 0, 1, 2, 3, 4, 5, or 6;
each s independently is 0 or 1 ; and
each z independently is 1 or 2
R7 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
R 8 is selected from the group consisting of H (hydrogen), -(CH2)„R C , optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
E is selected from the roup consisting of:
Figure imgf000011_0001
where Y is CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR14, where R14 is optionally substituted Ci-C8 alkyl, and Z is -F, -SR14, -N3, - NR14R14, -ONHR14, -OAc, or -OR14, where each R14 is independently H (hydrogen), Ci-Cs alkyl substituted Ci-C8 alkyl, or NRERF;
are each independently selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted Ci-Cg alkoxy, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl; and
J is selected from: CN, CHO, CH2OH, CH2F, CH2CN, CH2N3, COOH, CO- N(R15)OR15, CO-N(R15)CO-R15, CO-CO-NHR15, CO-N(R15)-S02R15, (CH2)pCOOH, (CH2)p-CH(OH)-COOH, CO-(CH2)p-COOH, CH=CH-COOH, CO- CH=CH-COOH, CH=CH-CONHOH, CH=CH-CONH-S02R, CO-CH=CH- CONHOH, B(OH)2, (CH2)p-B(OH)2, PO(OH)2, or (CH2)p-PO(OH)2, -R15-COOH, - CO-N(R15)OR15, -CO-N(R15)OR15, -R15-CO-N(R15)OR15, -R15-CO-NHR15, -R15-CO- N(R15)-S02R15, where each occurrence of R15 is independently selected from H (hydrogen), Ci-C8 alkyl, C3-C8 cycloalkyl, substituted Ci-C8 alkyl, substituted C3-C8 cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl and NRERF, and p is 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10.
BRIEF DESCRIPTION OF THE DRAWINGS
[0039] Figures 1-10 shows the cytotoxic effects of compounds or antibody drug conjugates (ADCs) on various cell types. The antibody used in the antibody drug conjugates is Trastuzumab.
DETAILED DESCRIPTION
[0040] Some embodiments provide a compound.
[0041] In some embodiments, the compound includes a linker.
[0042] In some embodiments, the compound includes a cytotoxic agent.
[0043] In some embodiments, the compound includes a functional group that has tubulin-binding properties or tubulin inhibitory properties.
[0044] In some embodiments, the compound includes a functional group that has protease inhibitory or efflux pump resistant properties. For example, the functional group may have proteasome inhibitory properties.
Definitions
[0045] As used herein, common organic abbreviations are defined as follows: Ac Acetyl
aq. Aqueous
BOC or Boc tert-Butoxycarbonyl
BrOP bromo tris(dimethylamino) phosphonium hexafluorophosphate
Bu n-Butyl
°C Temperature in degrees Centigrade
DCM methylene chloride
DEPC Diethylcyanophosphonate
DIC diisopropylcarbodiimide
DIEA Diisopropylethylamine
DMF N^-Dimethylformamide
EDC 1 -Ethyl-3 -(3 -dimethylaminopropyl)carbodiimide
Et Ethyl
EtOAc Ethyl acetate
Eq Equivalents
Fmoc 9-Fluorenylmethoxycarbonyl
g Gram(s)
h Hour (hours)
HATU 2-(lH-7-azabenzotriazol-l-yl)-l, l,3,3-tetramethyl uronium hexafluorophosphate
HOAt l-Hydroxy-7-azabenzotriazole
HOBT N-Hydroxybenzotriazole
HOSu N-Hydroxysuccinimide
HPLC High-performance liquid chromatography
LC/MS Liquid chromatography-mass spectrometry
Me Methyl
MeOH Methanol
MeCN Acetonitrile
mL Milliliter(s)
MS mass spectrometry
RP-HPLC reverse phase HPLC
rt room temperature
t-Bu tert-Butyl TEA Triethylamine
Tert, t tertiary
TFA Trifluoracetic acid
THF Tetrahydrofuran
THP Tetrahydropyranyl
TLC Thin-layer chromatography
μΐ, Microliter(s)
[0046] The term "pharmaceutically acceptable salt" refers to salts that retain the biological effectiveness and properties of a compound and, which are not biologically or otherwise undesirable for use in a pharmaceutical. In many cases, the compounds disclosed herein are capable of forming acid and/or base salts by virtue of the presence of amino and/or carboxyl groups or groups similar thereto. Pharmaceutically acceptable acid addition salts can be formed with inorganic acids and organic acids. Inorganic acids from which salts can be derived include, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like. Pharmaceutically acceptable base addition salts can be formed with inorganic and organic bases. Inorganic bases from which salts can be derived include, for example, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum, and the like; particularly preferred are the ammonium, potassium, sodium, calcium and magnesium salts. Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, basic ion exchange resins, and the like, specifically such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine. Many such salts are known in the art, as described in WO 87/05297, Johnston et al, published September 11 , 1987 (incorporated by reference herein in its entirety).
[0047] As used herein, "Ca to Cb" or "Ca_b" in which "a" and "b" are integers refer to the number of carbon atoms in the specified group. That is, the group can contain from "a" to "b", inclusive, carbon atoms. Thus, for example, a "Ci to C4 alkyl" or "Ci_4 alkyl" group refers to all alkyl groups having from 1 to 4 carbons, that is, CH3-, CH3CH2-, CH3CH2CH2-, (CH3)2CH-, CH3CH2CH2CH2-, CH3CH2CH(CH3)- and (CH3)3C-.
[0048] The term "halogen" or "halo," as used herein, means any one of the radio- stable atoms of column 7 of the Periodic Table of the Elements, e.g., fluorine, chlorine, bromine, or iodine, with fluorine and chlorine being preferred.
[0049] As used herein, "alkyl" refers to a straight or branched hydrocarbon chain that is fully saturated (i.e., contains no double or triple bonds). The alkyl group may have 1 to 20 carbon atoms (whenever it appears herein, a numerical range such as "1 to 20" refers to each integer in the given range; e.g., "1 to 20 carbon atoms" means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 20 carbon atoms, although the present definition also covers the occurrence of the term "alkyl" where no numerical range is designated). The alkyl group may also be a medium size alkyl having 1 to 9 carbon atoms. The alkyl group could also be a lower alkyl having 1 to 4 carbon atoms. The alkyl group may be designated as "Ci_4 alkyl" or similar designations. By way of example only, "Ci_4 alkyl" indicates that there are one to four carbon atoms in the alkyl chain, i.e., the alkyl chain is selected from the group consisting of methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl. Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, hexyl, and the like.
[0050] As used herein, "alkoxy" refers to the formula -OR wherein R is an alkyl as is defined above, such as "Ci_9 alkoxy", including but not limited to methoxy, ethoxy, n- propoxy, 1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy, sec-butoxy, and tert-butoxy, and the like.
[0051] As used herein, "alkylthio" refers to the formula -SR wherein R is an alkyl as is defined above, such as "Ci_9 alkylthio" and the like, including but not limited to methylmercapto, ethylmercapto, n-propylmercapto, 1-methylethylmercapto (isopropylmercapto), n-butylmercapto, iso-butylmercapto, sec-butylmercapto, tert- butylmercapto, and the like.
[0052] As used herein, "alkenyl" refers to a straight or branched hydrocarbon chain containing one or more double bonds. The alkenyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term "alkenyl" where no numerical range is designated. The alkenyl group may also be a medium size alkenyl having 2 to 9 carbon atoms. The alkenyl group could also be a lower alkenyl having 2 to 4 carbon atoms. The alkenyl group may be designated as "C2-4 alkenyl" or similar designations. By way of example only, "C2-4 alkenyl" indicates that there are two to four carbon atoms in the alkenyl chain, i.e., the alkenyl chain is selected from the group consisting of ethenyl, propen-l-yl, propen-2-yl, propen-3-yl, buten-l-yl, buten-2-yl, buten-3-yl, buten- 4-yl, 1-methyl-propen-l-yl, 2-methyl-propen-l-yl, 1-ethyl-ethen-l-yl, 2-methyl-propen-3-yl, buta-l,3-dienyl, buta-l,2,-dienyl, and buta-l,2-dien-4-yl. Typical alkenyl groups include, but are in no way limited to, ethenyl, propenyl, butenyl, pentenyl, and hexenyl, and the like.
[0053] As used herein, "alkynyl" refers to a straight or branched hydrocarbon chain containing one or more triple bonds. The alkynyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term "alkynyl" where no numerical range is designated. The alkynyl group may also be a medium size alkynyl having 2 to 9 carbon atoms. The alkynyl group could also be a lower alkynyl having 2 to 4 carbon atoms. The alkynyl group may be designated as "C2-4 alkynyl" or similar designations. By way of example only, "C2-4 alkynyl" indicates that there are two to four carbon atoms in the alkynyl chain, i.e., the alkynyl chain is selected from the group consisting of ethynyl, propyn-l-yl, propyn-2-yl, butyn-l-yl, butyn-3-yl, butyn-4-yl, and 2- butynyl. Typical alkynyl groups include, but are in no way limited to, ethynyl, propynyl, butynyl, pentynyl, and hexynyl, and the like.
[0054] The term "aromatic" refers to a ring or ring system having a conjugated pi electron system and includes both carbocyclic aromatic (e.g., phenyl) and heterocyclic aromatic groups (e.g., pyridine). The term includes monocyclic or fused-ring polycyclic (i.e., rings which share adjacent pairs of atoms) groups provided that the entire ring system is aromatic.
[0055] As used herein, "aryloxy" and "arylthio" refers to RO- and RS-, in which R is an aryl as is defined above, such as "C6-io aryloxy" or "C6-io arylthio" and the like, including but not limited to phenyloxy.
[0056] An "aralkyl" or "arylalkyl" is an aryl group connected, as a substituent, via an alkylene group, such as "C7_i4 aralkyl" and the like, including but not limited to benzyl, 2- phenylethyl, 3-phenylpropyl, and naphthylalkyl. In some cases, the alkylene group is a lower alkylene group (i.e., a Ci_4 alkylene group).
[0057] As used herein, "heteroaryl" refers to an aromatic ring or ring system (i.e., two or more fused rings that share two adjacent atoms) that contain(s) one or more heteroatoms, that is, an element other than carbon, including but not limited to, nitrogen, oxygen and sulfur, in the ring backbone. When the heteroaryl is a ring system, every ring in the system is aromatic. The heteroaryl group may have 5-18 ring members (i.e., the number of atoms making up the ring backbone, including carbon atoms and heteroatoms), although the present definition also covers the occurrence of the term "heteroaryl" where no numerical range is designated. In some embodiments, the heteroaryl group has 5 to 10 ring members or 5 to 7 ring members. The heteroaryl group may be designated as "5-7 membered heteroaryl," "5-10 membered heteroaryl," or similar designations. Examples of heteroaryl rings include, but are not limited to, furyl, thienyl, phthalazinyl, pyrrolyl, oxazolyl, thiazolyl, imidazolyl, pyrazolyl, isoxazolyl, isothiazolyl, triazolyl, thiadiazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, triazinyl, quinolinyl, isoquinlinyl, benzimidazolyl, benzoxazolyl, benzothiazolyl, indolyl, isoindolyl, and benzothienyl.
[0058] A "heteroaralkyl" or "heteroarylalkyl" is heteroaryl group connected, as a substituent, via an alkylene group. Examples include but are not limited to 2-thienylmethyl, 3-thienylmethyl, furylmethyl, thienylethyl, pyrrolylalkyl, pyridylalkyl, isoxazollylalkyl, and imidazolylalkyl. In some cases, the alkylene group is a lower alkylene group (i.e., a Ci_4 alkylene group).
[0059] As used herein, "carbocyclyl" means a non-aromatic cyclic ring or ring system containing only carbon atoms in the ring system backbone. When the carbocyclyl is a ring system, two or more rings may be joined together in a fused, bridged or spiro-connected fashion. Carbocyclyls may have any degree of saturation provided that at least one ring in a ring system is not aromatic. Thus, carbocyclyls include cycloalkyls, cycloalkenyls, and cycloalkynyls. The carbocyclyl group may have 3 to 20 carbon atoms, although the present definition also covers the occurrence of the term "carbocyclyl" where no numerical range is designated. The carbocyclyl group may also be a medium size carbocyclyl having 3 to 10 carbon atoms. The carbocyclyl group could also be a carbocyclyl having 3 to 6 carbon atoms. The carbocyclyl group may be designated as "C3-6 carbocyclyl" or similar designations. Examples of carbocyclyl rings include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclohexenyl, 2,3-dihydro-indene, bicycle[2.2.2]octanyl, adamantyl, and spiro[4.4]nonanyl.
[0060] A "(carbocyclyl)alkyl" is a carbocyclyl group connected, as a substituent, via an alkylene group, such as "C4_io (carbocyclyl)alkyl" and the like, including but not limited to, cyclopropylmethyl, cyclobutylmethyl, cyclopropylethyl, cyclopropylbutyl, cyclobutylethyl, cyclopropylisopropyl, cyclopentylmethyl, cyclopentylethyl, cyclohexylmethyl, cyclohexylethyl, cycloheptylmethyl, and the like. In some cases, the alkylene group is a lower alkylene group.
[0061] As used herein, "cycloalkyl" means a fully saturated carbocyclyl ring or ring system. Examples include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl.
[0062] As used herein, "cycloalkenyl" means a carbocyclyl ring or ring system having at least one double bond, wherein no ring in the ring system is aromatic. An example is cyclohexenyl.
[0063] As used herein, "heterocyclyl" means a non-aromatic cyclic ring or ring system containing at least one heteroatom in the ring backbone. Heterocyclyls may be joined together in a fused, bridged or spiro-connected fashion. Heterocyclyls may have any degree of saturation provided that at least one ring in the ring system is not aromatic. The heteroatom(s) may be present in either a non-aromatic or aromatic ring in the ring system. The heterocyclyl group may have 3 to 20 ring members (i.e., the number of atoms making up the ring backbone, including carbon atoms and heteroatoms), although the present definition also covers the occurrence of the term "heterocyclyl" where no numerical range is designated. The heterocyclyl group may also be a medium size heterocyclyl having 3 to 10 ring members. The heterocyclyl group could also be a heterocyclyl having 3 to 6 ring members. The heterocyclyl group may be designated as "3-6 membered heterocyclyl" or similar designations. In preferred six membered monocyclic heterocyclyls, the heteroatom(s) are selected from one up to three of O, N or S, and in preferred five membered monocyclic heterocyclyls, the heteroatom(s) are selected from one or two heteroatoms selected from O, N, or S. Examples of heterocyclyl rings include, but are not limited to, azepinyl, acridinyl, carbazolyl, cinnolinyl, dioxolanyl, imidazolinyl, imidazolidinyl, morpholinyl, oxiranyl, oxepanyl, thiepanyl, piperidinyl, piperazinyl, dioxopiperazinyl, pyrrolidinyl, pyrrolidonyl, pyrrolidionyl, 4-piperidonyl, pyrazolinyl, pyrazolidinyl, 1,3-dioxinyl, 1,3-dioxanyl, 1,4- dioxinyl, 1 ,4-dioxanyl, 1,3-oxathianyl, 1 ,4-oxathiinyl, 1 ,4-oxathianyl, 2H-l,2-oxazinyl, trioxanyl, hexahydro-l,3,5-triazinyl, 1,3-dioxolyl, 1,3-dioxolanyl, 1,3-dithiolyl, 1,3- dithiolanyl, isoxazolinyl, isoxazolidinyl, oxazolinyl, oxazolidinyl, oxazolidinonyl, thiazolinyl, thiazolidinyl, 1,3-oxathiolanyl, indolinyl, isoindolinyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydro-l,4-thiazinyl, thiamorpholinyl, dihydrobenzofuranyl, benzimidazolidinyl, and tetrahydroquinoline. [0064] A "(heterocyclyl)alkyl" is a heterocyclyl group connected, as a substituent, via an alkylene group. Examples include, but are not limited to, imidazolinylmethyl and indolinylethyl.
[0065] As used herein, "acyl" refers to -C(=0)R, wherein R is hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-1o aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein. Non- limiting examples include formyl, acetyl, propanoyl, benzoyl, and acryl.
[0066] An "O-carboxy" group refers to a "-OC(=0)R" group in which R is selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5- 10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0067] A "C-carboxy" group refers to a "-C(=0)OR" group in which R is selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5- 10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein. A non- limiting example includes carboxyl (i.e., -C(=0)OH).
[0068] A "cyano" group refers to a "-CN" group.
[0069] A "cyanato" group refers to an "-OCN" group.
[0070] An "isocyanato" group refers to a "-NCO" group.
[0071] A "thiocyanato" group refers to a "-SCN" group.
[0072] An "isothiocyanato" group refers to an "-NCS" group.
[0073] A "sulfmyl" group refers to an "-S(=0)R" group in which R is selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0074] A "sulfonyl" group refers to an "-S02R" group in which R is selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3_7 carbocyclyl, C6_io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0075] An "S-sulfonamido" group refers to a "-S02NRARB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0076] An "N-sulfonamido" group refers to a "-N(RA)S02RB" group in which RA and Rb are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3_7 carbocyclyl, C6_io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein. [0077] An "O-carbamyl" group refers to a "-OC(=0)NRARB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0078] An "N-carbamyl" group refers to an "-N(RA)C(=0)ORB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0079] An "O-thiocarbamyl" group refers to a "-OC(=S)NRARB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0080] A "urea" group refers to a "-N(RA)C(=0)NRARB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0081] An "N-thiocarbamyl" group refers to an "-N(RA)C(=S)ORB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_ 6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0082] A "C-amido" group refers to a "-C(=0)NRARB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0083] An "N-amido" group refers to a "-N(RA)C(=0)RB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3-7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein.
[0084] An "amino" group refers to a "-NRARB" group in which RA and RB are each independently selected from hydrogen, Ci_6 alkyl, C2_6 alkenyl, C2_6 alkynyl, C3_7 carbocyclyl, C6-io aryl, 5-10 membered heteroaryl, and 5-10 membered heterocyclyl, as defined herein. A non- limiting example includes free amino (i.e., -NH2). [0085] An "aminoalkyl" group refers to an amino group connected via an alkylene group.
[0086] An "alkoxyalkyl" group refers to an alkoxy group connected via an alkylene group, such as a "C2-8 alkoxyalkyl" and the like.
[0087] As used herein, a substituted group is derived from the unsubstituted parent group in which there has been an exchange of one or more hydrogen atoms for another atom or group. Unless otherwise indicated, when a group is deemed to be "substituted," it is meant that the group is substituted with one or more subsitutents independently selected from Ci-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C3-C7 carbocyclyl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), C3-C7-carbocyclyl- Ci-C6-alkyl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), 5-10 membered heterocyclyl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), 5-10 membered heterocyclyl- Ci-C6-alkyl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), aryl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), aryl(Ci-C6)alkyl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), 5-10 membered heteroaryl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), 5-10 membered heteroaryl(Ci-Ce)alkyl (optionally substituted with halo, Ci-C6 alkyl, Ci-C6 alkoxy, Ci-C6 haloalkyl, and Ci-C6 haloalkoxy), halo, cyano, hydroxy, Ci-C6 alkoxy, Ci-C6 alkoxy(Ci-C6)alkyl (i.e., ether), aryloxy, sulfhydryl (mercapto), halo(Ci- C6)alkyl (e.g., -CF3), halo(Ci-C6)alkoxy (e.g., -OCF3), Ci-C6 alkylthio, arylthio, amino, amino(Ci-C6)alkyl, nitro, O-carbamyl, N-carbamyl, O-thiocarbamyl, N-thiocarbamyl, C- amido, N-amido, S-sulfonamido, N-sulfonamido, C-carboxy, O-carboxy, acyl, cyanato, isocyanato, thiocyanato, isothiocyanato, sulfmyl, sulfonyl, and oxo (=0). Wherever a group is described as "optionally substituted" that group can be substituted with the above substituents.
[0088] It is to be understood that certain radical naming conventions can include either a mono-radical or a di-radical, depending on the context. For example, where a substituent requires two points of attachment to the rest of the molecule, it is understood that the substituent is a di-radical. For example, a substituent identified as alkyl that requires two points of attachment includes di-radicals such as -CH2-, -CH2CH2-, -CH2CH(CFi3)CFi2-, and the like. Other radical naming conventions clearly indicate that the radical is a di-radical such as "alkylene" or "alkenylene."
[0089] When two R groups are said to form a ring (e.g., a carbocyclyl, heterocyclyl, aryl, or heteroaryl ring) "together with the atom to which they are attached," it is meant that the collective unit of the atom and the two R groups are the recited ring. The ring is not otherwise limited by the definition of each R group when taken individually. For example, when the following substructure is present:
Figure imgf000022_0001
and R1 and R2 are defined as selected from the group consisting of hydrogen and alkyl, or R1 and R2 together with the nitrogen to which they are attached form a heterocyclyl, it is meant that R1 and R2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure:
Figure imgf000022_0002
where ring E is a heteroaryl ring containing the depicted nitrogen.
[0090] Similarly, when two "adjacent" R groups are said to form a ring "together with the atom to which they are attached," it is meant that the collective unit of the atoms, intervening bonds, and the two R groups are the recited ring. For example, when the following substructure is present:
Figure imgf000022_0003
and R1 and R2 are defined as selected from the group consisting of hydrogen and alkyl, or R1 and R2 together with the atoms to which they are attached form an aryl or carbocylyl, it is meant that R1 and R2 can be selected from hydrogen or alkyl, or alternatively, the substructure has structure:
Figure imgf000023_0001
where E is an aryl ring or a carbocylyl containing the depicted double bond.
[0091] Wherever a substituent is depicted as a di-radical (i.e., has two points of attachment to the rest of the molecule), it is to be understood that the substituent can be attached in any directional configuration unless otherwise indicated. Thus, for example, a substituent depicted as -AE- or v ¾ A\ E A includes the substituent being oriented such that the A is attached at the leftmost attachment point of the molecule as well as the case in which A is attached at the rightmost attachment point of the molecule.
[0092] "Subject" as used herein, means a human or a non-human mammal, e.g., a dog, a cat, a mouse, a rat, a cow, a sheep, a pig, a goat, a non-human primate or a bird, e.g., a chicken, as well as any other vertebrate or invertebrate.
Compounds
[0093] The skilled artisan will recognize that some structures described herein may be resonance forms or tautomers of compounds that may be fairly represented by other chemical structures, even when kinetically; the artisan recognizes that such structures may only represent a very small portion of a sample of such compound(s). Such compounds are considered within the scope of the structures depicted, though such resonance forms or tautomers are not represented herein.
[0094] Isotopes may be present in the compounds described. Each chemical element present in a compound either specifically or generically described hereinmay include any isotope of said element. For example, in a compound specifically or generically described herein a hydrogen atom may be explicitly disclosed or understood to be present in the compound and each such hydrogen atom is any isotope of hydrogen, including but not limited to hydrogen-1 (protium) and hydrogen-2 (deuterium). Thus, reference herein to a compound encompasses all potential isotopic forms unless the context clearly dictates otherwise.
Utilities and applications
[0095] Some embodiments provide a method of treating a patient in need thereof comprising administering a compound as disclosed and described herein to said patient. In some embodiments, the patient may have cancer, an infection, or an immune system disease. In some embodiments, the compound may have anti-tumor, antibiotic, or anti-inflammatory activity.
Structures
[0096] Some embodiments provide a compound having the structure
Figure imgf000024_0001
[0097] or a pharmaceutically acceptable salt thereof, wherein: A is a tubulin binding moiety; B is a group might have protease inhibitory or efflux pump resistant properties; and Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, substituted or cyclic Ci-Cg alkyl, aryl, and substituted aryl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally R7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring. In some embodiments, the compound may be used alone as API (active pharmaceutical ingredient) or in a prodrug form. In some embodiments, the compound may be included in a conjugate including a linker and another component. In some embodiments, the compound may be included in a conjugate including a linker and a targeting moiety, such as antibody, Fab, peptide, protein ligand, and the like. In some embodiments, the compound may be included in a conjugate including a linker and a carrier molecule, such as HSA, lipid, polymers, nanoparticles, and the like. In some embodiments, the compound may be included in a conjugate including a linker and a small molecule drug/ligand, such as folic acid.
[0098] As used herein, the term "tubulin binding moiety" refers to a structural component of a compound that inhibits tubulin polymerization under a certain set of conditions. In some embodiments, the compound may inhibit tubulin polymerization under in vivo or in vitro conditions. For example, the compound may inhibit tubulin polymerization in PBS. Examples of compounds that inhibit tubulin polymerization are described in Peltier, et al, "The Total Synthesis of Tubulysin D," J. Am. Chem. Soc, 2006, 128 (50): 16018-16019, and U.S. Publication No.: 2005/0239713 the disclosures of which are incorporated herein by reference in their entirety. [0099] As used herein, the term "functional moiety" refers to a structural component of a compound that interacts with a biological moiety or fragment of the biological moiety under a certain set of conditions. In some embodiments, the functional moiety may interact with a biological moiety or fragment of the biological moiety under in vivo or in vitro conditions. For example, the functional moiety may interact with a biological moiety or fragment of the biological moiety in PBS. In some embodiments, the functional moiety may afford a desirable effect in a compound comparison to a compound that does not include the functional moiety. In some embodiments, the functional moiety may contribute to enzyme inhibition or efflux pump resistance in a compound.
[0100] In some embodiments, the cytotoxic compound having the structure of Formula la:
Figure imgf000025_0001
(la)
[0101] or a pharmaceutically acceptable salt thereof,
[0102] wherein,
[0103] B is a moiety might have contribution to enzyme inhibition or efflux pump resistance;
[0104] Ri-R.8 are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0105] Y is CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR, where R is Ci-Cg alkyl or substituted Ci-Cg alkyl.
[0106] In some embodiments, B may be CN, CHO, CH2OH, CH2F, CH2CN, CH2N3, COOH, CO-NHOH, CO-CO-NHR, CO-NH-S02R, (CH2)nCOOH, (CH2)n-CH(OH)- COOH, CO-(CH2)n-COOH, CH=CH-COOH, CO-CH=CH-COOH, CH=CH-CONHOH, CO- CH=CH-CONHOH, B(OH)2, (CH2)n-B(OH)2, PO(OH)2, or (CH2)n-PO(OH)2, where R is Ci-Cg alkyl or substituted Ci-Cg alkyl, and n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
[0107] In some embodiments, the dual active compound having the structure of Formula I has the structure of Formula lb:
Figure imgf000026_0001
(lb)
[0108] or a pharmaceutically acceptable salt thereof,
[0109] B is a moiety might have contribution to enzyme inhibition or efflux pump resistance;
[0110] Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally R7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0111] Z is -F, -SR, -N3, -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-Cg alkyl or substituted Ci-Cg alkyl
[0112] In some embodiments, B may be CN, CHO, CH2OH, CH2F, CH2CN, CH2N3, COOH, CO-NHOH, CO-CO-NHR, CO-NH-S02R, (CH2)nCOOH, (CH2)n-CH(OH)- COOH, CO-(CH2)n-COOH, CH=CH-COOH, CO-CH=CH-COOH, CH=CH-CONHOH, CO- CH=CH-CONHOH, B(OH)2, (CH2)n-B(OH)2, PO(OH)2, or (CH2)n-PO(OH)2, where R = Ci- C8 alkyl or substituted Ci-Cg alkyl, and n is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
[0113] Some embodiments provide a compound having the structure of Formula
Ila:
Figure imgf000026_0002
[0114] or a pharmaceutically acceptable salt thereof,
[0115] wherein X is OR10, selected from, but not limited to, a group consisting of at least one hetero atom:
Figure imgf000027_0001
(IIa-2)
[0117] Ri-Rio are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, , or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally and respectively R7, Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0118] X is a group consisting of at least one heteroatom;
[0119] Y is CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR, where R is Ci-Cg alkyl or substituted Ci-Cg alkyl.
[0120] In some embodiments, the dual active compound having the structure of Formula I has the structure of Formula lib:
Figure imgf000027_0002
[0121] or a pharmaceutically acceptable salt thereof,
[0122] wherein, n is 0 or 1 ; X is OR10, selected from, but not limited to, a group consisting of at least one hetero atom:
Figure imgf000028_0001
(IIb-1)
[0123] wherein, n is 0 or 1 ;; XX iis S02R , selected from, but not limited to, a group consistin of at least one hetero atom:
Figure imgf000028_0002
(IIb-2)
[0124] Ri-Rio are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, and substituted or cyclic Ci-Cg alkyl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7- membered ring, or optionally and respectively R7, Rs and R9 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring;
[0125] X is a group of at least one heteroatom;
[0126] Z is -F, -SR, -N3, -NRR, -ONHR, -OAc, or -OR, where each R is independently H, Ci-C8 alkyl or substituted Ci-C8 alkyl
[0127] Examples of compounds having the structure of Formula la include but not limited to the following:
Figure imgf000028_0003
1a 2a
Figure imgf000029_0001
-28- [0129] Examples of general compounds having the structure of Formula la include the following:
Figure imgf000030_0001
3a-k 4a-k
[0130] Examples of compounds having the structure of Formula la include the following:
Figure imgf000030_0002
3e 4e [0131] Examples of general compounds having the structure of Formula la include the following:
Figure imgf000031_0001
[0132] Examples of compounds having the structure of Formula la include the following:
Figure imgf000031_0002
5d 6d
Figure imgf000032_0001
5e 6e
[0133] Examples of general compounds having the structure of Formula la include the following:
Figure imgf000032_0002
7a-k 8a-k
[0134] Examples of compounds having the structure of Formula la include the following:
Figure imgf000032_0003
7e 8e [0135] Examples of general compounds having the structure of Formula la include the following:
Figure imgf000033_0001
9a-e 15a-e
[0136] Examples of compounds having the structure of Formula la include the following:
Figure imgf000033_0002
-e
Figure imgf000033_0003
14a-e 20a-e
[0137] Examples of general compounds having the structure of Formula la include the following: H
OMe O OMe O CN O OMe O OMe O
O
21a-e 27a-e
[0138] Examples of compounds having the structure of Formula la include the following:
Figure imgf000034_0001
22a-e 28a-k
Figure imgf000034_0002
23a-e
Figure imgf000034_0003
25a-k 31a-k
Figure imgf000034_0004
26a-e 32a-k
[0139] Examples of general compounds having the structure of Formula la include the following:
Figure imgf000034_0005
33a-q 38a-q [0140] Examples of compounds having the structure of Formula la include the following:
Figure imgf000035_0001
37a-q 42
[0141] Examples of compounds having the structure of Formula lb include the following:
Figure imgf000036_0001
[0142] Examples of compounds having the structure of Formula lb include the following:
Figure imgf000037_0001
[0143] In some embodiments, the compound is conjugated to a targeting moiety.
[0144] In some embodiments, the targeting moiety includes a monoclonal antibody (mAB). In some embodiments, the compound includes a spacer or a multifunctional linker.
[0145] In some embodiments, the spacer connects to the mAB by a group including a N (nitrogen) atom. In some embodiments, the multifunctional linker connects to the mAB by a group including a N (nitrogen) atom. In some embodiments, the spacer or multifunctional linker may be optionally connected to an auxiliary moiety. In some embodiments, the auxiliary moiety may be a second targeting moiety such as mAB and peptide. In some embodiments, the auxiliary moiety may be a hydrophilic polymer such as polyethylene glycol (PEG), and the like. In some embodiments, the spacer or multifunctional linker may include a group including a N (nitrogen) atom. In some embodiments, the spacer or multifunctional linker may include a cyclic group including a N (nitrogen) atom.
[0146] In some embodiments, the spacer connects to the mAB by a sulfide bond. In some embodiments, the multifunctional linker connects to the mAB by a sulfide bond. In some embodiments, the spacer or multifunctional linker may be optionally connected to an auxiliary moiety. In some embodiments, the auxiliary moiety may be a second targeting moiety such as mAB and peptide. In some embodiments, the auxiliary moiety may be a hydrophilic polymer such as polyethylene glycol (PEG), and the like. In some embodiments, the spacer or multifunctional linker may include a 2- to 5- atom bridge. In some embodiments, the spacer or multifunctional linker may include a 4C bridge.
Conjugation methods, spacers and linkers involved
[0147] Some embodiments provide a method of conjugating of a targeting moiety through a spacer or a multifunctional linker.
[0148] In some embodiments, the spacer or multifunctional linker may include a 2- to 5- atom bridge. In some embodiments, the method includes a single-step or sequential conjugation approach. In some embodiments, the compound includes a spacer or a multifunctional linker. In some embodiments, the spacer or multifunctional linker may include a noncleavable or cleavable unit such as peptides.
[0149] In some embodiments, the spacer or multifunctional linker may include a group including a N (nitrogen) atom. In some embodiments, the method includes a single- step or sequential conjugation approach. In some embodiments, the spacer or multifunctional linker may include a noncleavable or cleavable unit such as a peptide.
[0150] Some embodiments provide a compound-conjugate having the structure of Formula Ila:
Figure imgf000039_0001
(Ila)
or a pharmaceutically acceptable salt thereof, wherein:
R^R9 are each independently selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl, or optionally R1 and R2 together with the nitrogen to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R1 and R3 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7- membered ring, or optionally R7, R8 and R9 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R1 is R1A or R1B;
R1A comprises a targeting moiety;
R1B is -L1(CH2)nRc, -L10(CH2)nRc or -(CH2)nRc;
R is Ci-Cg alkyl, C3-C8 cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R , or optionally R comprises a targeting moiety;
each RD is independently selected from the group consisting of -OH, -N3, halo, cyano, nitro, -(CH2)nNRERF, -(CH2)nC(=0)NRERF, — 0(CH2)nNRERF, -0(CH2)nC(=0)NRERF, -0(CH2)mOC(=0)NRERF, -NRGC(=0)RH, -NRGS(0)zRH, -0(CH2)mO(CH2)mRJ, -0(CH2)nC(=0)RJ, -0(CH2)nRJ, optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, and optionally substituted -0-(d-C8 alkyl);
each NRERF is independently selected, wherein RE and RF are each independently selected from hydrogen, -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]- [L1(C(R2A)2)r(NR2A)s(C(R2A)2)R]S-(L1)s-RJ, -[(LW ^ NR24),^ ),]- (L1)s[(C(R2A)2)rO(C(R2A)2)r(L2)s]s-(L1)s-RJ, optionally substituted d_8 alkyl, optionally substituted C3-8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each R is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally substituted heterocyclyl;
each RH is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or -NRERF;
each RJ is independently selected from the group consisting of hydrogen, optionally substituted Ci-C8 alkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)„OR2B, -0(CH2)„OR2B, — (CH2)nNR2BR2B, -C(R2A)2NR2BR2B, -(CH2)nC(=0)OR2B, and -C(=0)NHR2B;
each R2A is independently selected, wherein R2A is selected from the group consisting of hydrogen, halo, -OH, optionally substituted Ci-Cg alkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)nOR2B, -(CH2)nNR2CR2C, -C(=0)OR2B, -C(=0)NR2CR2C, or optionally two geminal R2A and the carbon to which they are attached are together an optionally substituted three- to six-membered carbocyclic ring;
each R2B is independently selected from the group consisting of hydrogen, -OH, -(CH2)„C(=0)OH, -C(=0)(C(R2D)2)„L3R2E, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each NR R is independently selected, wherein each R is independently selected from the group consisting of hydrogen, -OH, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, or optionally both R together with the nitrogen to which they are attached are an optionally substituted heterocyclyl; each R is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each R2E is independently selected from the group consisting of optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, and -(CH2)nC(=0)OR2F;
each R2F is independently selected from the group consisting hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L1 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0- -C(=0)NR2A- -S(=0)NR2A- -S(=0)2NR2A- -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each L2 is independently selected from the group consisting of optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L3 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0- -C(=0)NR2A- -S(=0)NR2A-, -S(=0)2NR2A-, -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each m independently is 1 or 2;
each n independently is 0, 1, 2, 3, 4, 5, or 6;
each r independently is 0, 1, 2, 3, 4, 5, or 6;
each s independently is 0 or 1 ; and
each z independently is 1 or 2
R7 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
R 8 is selected from the group consisting of H (hydrogen), -(CH2)„R C , optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl; X is a group consisting of at least one heteroatom, or selected from groups consisting of -OR10, -S02-R10, where R10 is Rc
[0151] In some embodiments, the active compound having the structure of Formula I has the structure of Formula lib:
Figure imgf000042_0001
[0152] or a pharmaceutically acceptable salt thereof,
wherein:
R9 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, substituted Ci-Cg alkyl, substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally R7, R8 and R9 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring,
X is selected from groups consisting of -OR10, -S02-R10, where R10 is Rc; and n is 0 or 1.
[0153] In some embodiments, at least one of R1, R10 and X comprises a targeting moiety. In some embodiments, at least one of R1, R10 and X further comprises a linker. In some embodiments, at least one of R1, R10 and X comprises -(CH2)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, at least one of R1, R10 and X comprises - (CH2CH20)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, at least one of R1, R10 and X comprises Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu-Lys, Gly- Gly-Arg, or Ala-Ala-Asn-PAB. In some embodiments, at least one of R1, R10 and X comprises a peptide, oligosaccharide, -(CH2)„-, -(CH2CH20)n-, Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu-Lys, Gly-Gly-Arg, Ala-Ala-Asn-PAB, or combinations thereof. In some embodiments, the targeting moiety is a monoclonal antibody (mAB). In some embodiments, the targeting moiety is an antibody fragment, surrogate, or variant. In some embodiments, the targeting moiety is a protein ligand. In some embodiments, the targeting moiety is a protein scaffold. In some embodiments, the targeting moiety is a peptide. In some embodiments, the targeting moiety is a small molecule ligand. In some embodiments, the linker includes a 4-carbon bridge and at least two sulfur atoms. In some embodiments, the linker includes a fragment selected from the group consisting of:
Figure imgf000043_0001
[0154] In some embodiments at least one of R1, R10 and X comprises
Figure imgf000043_0002
, wherein:
the A-component is the targeting moiety; the E-component is an optionally substituted heteroaryl or an optionally substituted heterocyclyl; L3 is an optionally substituted Ci-C6 alkyl, or L3 is null, when L3 is null the sulfur is directly connected to the E-component; and L4 is an optionally substituted Ci-C6 alkyl, or L4 is null, when L4 is null the sulfur is directly connected to the E-component. In some embodiments, the E-component includes a fragment selected from the group consisting of:
Figure imgf000043_0003
In some embodiments, L is -(CH2)-; and L is -(CH2)-. In some embodiments, L is null; and L4 i iss nnuullll..
[0155] In some embodiments,
Figure imgf000043_0004
Figure imgf000044_0001
[0156] In some embodiments, at least one ofR1, R10 and X comprises:
Figure imgf000044_0002
wherein: A is the targeting moiety; X is N (nitrogen) or CH; Y is N (nitrogen), or CH; m is 0, 1, or 2; L is a linker, or null; and L1A is a linker, or null. In some embodiments, L is null. In some embodiments, L includes -C(=0)-, -NH-C(=0)-, -C(=0)-0- -NH-C(=0)-NH- or -NH-C(=0)-0-. In some embodiments, L is -C(=0)-, -NH-C(=0)-, -C(=0)-0- - NH-C(=0)-N - or -NH-C(=0)-0-. In some embodiments, L is -C(=0)-. In some
embodiments,
Figure imgf000044_0003
is
[0157] In some embodiments, at least one of R1, R10 and X comprises, consists of, ists essentially of:
Figure imgf000044_0004
Figure imgf000045_0001
wherein L may be optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L5 is Ci-Cg alkyl.
[0158] In some embodiments, at least one of R1, R10 and X comprises, consists of, or consist essentially of:
Figure imgf000045_0002
, wherein A is the targeting moiety, L may be optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L5 is Ci-Cg alkyl.
[0159] In some embodiments, at least one of R1, R10 and X comprises, consists of, or consist essentially of:
Figure imgf000046_0001
, wherein A is the targeting moiety, L5 may be optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted Ci-C8 alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L5 is Ci-Cg alkyl. L6 may be H, optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
[0160] In some embodiments, at least one of R1, R10 and X comprises, consists of, or consist essentially of:
Figure imgf000046_0002
, wherein A is the targeting moiety, L5 may be optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted C3-C8 cylcoalkyl annulated to cyclooctyl ring, optionally substituted Ci-C8 alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted Ci-C8 alkyl. In some embodiments, L5 is Ci-C8 alkyl.
[0161] Some embodiments provide a compound-conjugate having the structure of Formula V:
Figure imgf000046_0003
(V)
[0162] or a pharmaceutically acceptable salt thereof, wherein: A1 may be a targeting moiety; B1 is an auxiliary moiety that optionally includes a second targeting moiety, or B1 is null; L1 includes a group including a N (nitrogen) atom or a group including a 2- to
5 -carbon bridge and at least one sulfur atom; each D is independently selected, where each D includes a compound; each L2 is independently a linker, wherein at least one L2 links to L1; and n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, A1 may be a monoclonal antibody (mAB). In some embodiments, A1 may be an antibody fragment, surrogate, or variant. In some embodiments, A1 may be a protein ligand. In some embodiments, A1 may be a protein scaffold. In some embodiments, A1 may be a peptide. In some embodiments, A1 may be RNA or DNA. In some embodiments, A1 may be a RNA or DNA fragment. In some embodiments, A1 may be a small molecule ligand. In some embodiments, B1 may be a hydrophilic polymer. In some embodiments, the hydrophilic polymer may polyethylene glycol (PEG), and the like. In some embodiments, B1 may be a biodegradable polymer. In some embodiments, the biodegradable polymer may be unstructured proteins polyamino acids, polypeptides polysaccharides and combinations thereof. In some embodiments, B1 may be a monoclonal antibody (mAB). In some embodiments, B1 may be an antibody fragment, surrogate, or variant. In some embodiments, B1 may be a protein ligand. In some embodiments, B1 may be a protein scaffold. In some embodiments, B1 may be a peptide. In some embodiments, B1 may be RNA or DNA. In some embodiments, B1 may be a RNA or
DNA fragment. In some embodiments, B1 may be a small molecule ligand. In some embodiments, D may includes a biologically active compound. In some embodiments, D may includes a core from tubulin-binder or tubulin-binder derivative. In some embodiments, D include a core from epothilone A, epothilone B, paclitaxel, or derivatives thereof. In some embodiments, D includes
Figure imgf000047_0001
, wherein: A is a tubulin binding moiety; B is a protease inhibition moiety; and Ri-Rs are each independently selected from the group consisting of H (hydrogen), Ci-Cg alkyl, substituted or cyclic Ci-Cg alkyl, aryl, and substituted aryl, or optionally Ri and R2 together with the nitrogen to which they are attached are a cyclic 5- to 7-membered ring, or optionally Ri and R3 together with the atoms to which they are attached are a cyclic 5- to 7-membered ring, or optionally R7 and Rs together with the atoms to which they are attached are a cyclic 5- to 7-membered ring. In some embodiments A may be
Figure imgf000048_0001
; and Y may be CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-
OH, CH-ONH2, or CHOR, where R is Ci-C8 alkyl or substituted Ci-C8 alkyl. In some
embodiments, A may be
Figure imgf000048_0002
; may be N (nitrogen), CH, C-OH, C-OR,
CSH, CSR, where R is Ci-C8 alkyl or substituted Ci-C8 alkyl; X may be F, OH, N3, OMe, or OR, where R is Ci-Cg alkyl or substituted Ci-Cg alkyl; and Y may be CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR, where R is CrC8 alkyl or substituted Ci-C8 alkyl. In some embodiments, L2 may include a spacer or a multifunctional linker. In some embodiments, L2 may include a spacer and a multifunctional linker. In some embodiments, L2 may include a multifunctional linker. In some embodiments, each L2 may be a linker, wherein the linker may be cleavable or non-cleavable under biological conditions. In some embodiments, the linker may be cleavable by an enzyme. In some embodiments, L2 may include Linker. In some embodiments, L1 includes a cyclic group including at least one N (nitrogen) atom. In some embodiments, L1 includes a cyclic group including at least two N (nitrogen) atoms. In some embodiments, L1 includes a cyclic group including at least one N (nitrogen) atom and a spacer. In some embodiments, L1 includes a cyclic group including at least two N (nitrogen) atoms and a spacer. In some embodiments, the spacer connects to the mAB by an amide bond. In some embodiments, the spacer connects to the mAB through an amine bond. In some embodiments, L1 includes a 2- to 5- carbon bridge and at least one sulfur atom. In some embodiments, L1 includes a 2- to 5- carbon bridge and at least two sulfur atoms. In some embodiments, L1 includes a 2- to 5- carbon bridge and a spacer. In some embodiments, L1 includes a 2- to 5 -carbon bridge, at least two sulfur atoms and a spacer. In some embodiments, L1 may include one or more sulfurs. In some embodiments, the L1 may include two or more sulfurs. In some embodiments, the L1 may include exactly two sulfurs. In some embodiments, may include a 4-carbon bridge and/or a spacer. In some embodiments, L1 include a 4-carbon bridge or a spacer. In some embodiments, L1 may include a 4-carbon bridge and a spacer. In some embodiments, L1 includes a 4-carbon bridge and at least two sulfur atoms. In some embodiments, the spacer connects to the mAB by a sulfide bond. In some embodiments, the spacer connects to the mAB through a thioether. In some embodiments, A1 comprises at least one modified n-butyl L-a-amino acid. In some embodiments, at least one modified L-Lysine residue is from an L-Lysine residue of a peptide before conjugation. In some embodiments, at least one nitrogen of L1 is from an at least one modified n-butyl L-a-amino acid of a peptide before conjugation. In some embodiments, A1 and L1 together comprise at least one modified L-Lysine residue. In some embodiments, the terminal nitrogen of the side chain of an L- Lysine residue of a peptide before conjugation is the at least one N (nitrogen) atom of L1. In some embodiments, A1 comprises the -(CH2)4- of the side chain of an L-Lysine residue of a peptide before conjugation that provides the at least one N (nitrogen) atom of L1. In some embodiments, A1 comprises a modified n-butyl a-amino acid residue. In some embodiments, Linker may be a peptide. In some embodiments, Linker may include an oligosaccharide. For example, Linker may include chitosan. In some embodiments, L2 may include Linker and - (CH2)„- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, L2 may include Linker and -(CH2CH20)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, Linker may include -(CH2)„- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, Linker may include -(CH2CH20)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, Linker may include Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu- Lay, Gly-Gly-Arg, Ala-Ala-Asn-PAB, or the like. In some embodiments, Linker may include any combination of peptide, oligosaccharide, -(CH2)„-, -(CH2CH20)n-, Val-Cit-PAB, Val-Ala-PAB, Phe-Lys-PAB, D-Val-Leu-Lay, Gly-Gly-Arg, Ala-Ala-Asn-PAB, and the like. In some embodiments, the spacer may include a peptide. In some embodiments, the spacer may include an oligosaccharide. For example, the spacer may include chitosan. In some embodiments, the spacer may include -(CH2)„- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, L1 may include a component including a 4-carbon bridge and -(CH2)„- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the spacer may include - (CH2CH20)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, L1 may include a component including a 4-carbon bridge and -(CH2CH20)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the spacer may include Val-Cit-PAB, Val-Ala-PAB, Phe- Lys-PAB, Ala-Ala-Asn-PAB, or the like. In some embodiments, the spacer may be any combination of peptide, oligosaccharide, -(CH2)„-, -(CH2CH20)n-, Val-Cit-PAB, Val-Ala- PAB, Phe-Lys-PAB, Ala-Ala-Asn-PAB, and the like. In some embodiments, L1 may include,
Figure imgf000050_0001
Figure imgf000050_0002
[0163] In some embodiments, the compound-conjugates may include one or more components selected from the group consisting of an amino acid, an amino acid residue, an amino acid analog, and a modified amino acid.
[0164] As used herein, the term "peptide" refers to a structure including one or more components each individually selected from the group consisting of an amino acid, an amino acid residue, an amino acid analog, and a modified amino acid. The components are typically joined to each other through an amide bond.
[0165] As used herein, the term "amino acid" includes naturally occurring amino acids, a molecule having a nitrogen available for forming an amide bond and a carboxylic acid, a molecule of the general formula NH2-CHR-COOH or the residue within a peptide bearing the parent amino acid, where "R" is one of a number of different side chains. "R" can be a substituent found in naturally occurring amino acids. "R" can also be a substituent referring to one that is not of the naturally occurring amino acids.
[0166] As used herein, the term "amino acid residue" refers to the portion of the amino acid which remains after losing a water molecule when it is joined to another amino acid.
[0167] As used herein, the term "amino acid analog" refers to a structural derivative of an amino acid parent compound that often differs from it by a single element. [0168] As used herein, the term "modified amino acid" refers to an amino acid bearing an "R" substituent that does not correspond to one of the twenty genetically coded amino acids.
[0169] As used herein, the abbreviations for the genetically encoded L- enantiomeric amino acids are conventional and are as follows: The D-amino acids are designated by lower case, e. g. D-proline = p, etc.
TABLE 1
Amino Acids One-Letter Symbol Common Abbreviation
Alanine A Ala
Arginine R Arg
Asparagine N Asn
Aspartic acid D Asp
Cysteine C Cys
Glutamine Q Gin
Glutamic acid E Glu
Glycine G Gly
Histidine H His
Isoleucine I lie
Leucine L Leu
Lysine K Lys
Phenylalanine F Phe
Proline P Pro
Serine S Ser
Threonine T Thr
Tryptophan w Trp
Tyrosine Y Tyr
Valine V Val
[0170] Certain amino acid residues in the compound-conjugate can be replaced with other amino acid residues without significantly deleteriously affecting, and in many cases even enhancing, the activity of the peptides. Thus, also contemplated by the preferred embodiments are altered or mutated forms of the active agent-conjugate wherein at least one defined amino acid residue in the structure is substituted with another amino acid residue or derivative and/or analog thereof. It will be recognized that in preferred embodiments, the amino acid substitutions are conservative, i.e., the replacing amino acid residue has physical and chemical properties that are similar to the amino acid residue being replaced.
[0171] For purposes of determining conservative amino acid substitutions, the amino acids can be conveniently classified into two main categories—hydrophilic and hydrophobic—depending primarily on the physical-chemical characteristics of the amino acid side chain. These two main categories can be further classified into subcategories that more distinctly define the characteristics of the amino acid side chains. For example, the class of hydrophilic amino acids can be further subdivided into acidic, basic and polar amino acids. The class of hydrophobic amino acids can be further subdivided into nonpolar and aromatic amino acids. The definitions of the various categories of amino acids are as follows:
[0172] The term "hydrophilic amino acid" refers to an amino acid exhibiting a hydrophobicity of less than zero according to the normalized consensus hydrophobicity scale of Eisenberg et al., 1984, J. Mol. Biol. 179: 125-142. Genetically encoded hydrophilic amino acids include Thr (T), Ser (S), His (H), Glu (E), Asn (N), Gin (Q), Asp (D), Lys (K) and Arg (R).
[0173] The term "hydrophobic amino acid" refers to an amino acid exhibiting a hydrophobicity of greater than zero according to the normalized consensus hydrophobicity scale of Eisenberg, 1984, J. Mol. Biol. 179:1.25-142. Genetically encoded hydrophobic amino acids include Pro (P), He (I), Phe (F), Val (V), Leu (L), Trp (W), Met (M), Ala (A), Gly (G) and Tyr (Y).
[0174] The term "acidic amino acid" refers to a hydrophilic amino acid having a side chain pK value of less than 7. Acidic amino acids typically have negatively charged side chains at physiological pH due to loss of a hydrogen ion. Genetically encoded acidic amino acids include Glu (E) and Asp (D).
[0175] The term "basic amino acid" refers to a hydrophilic amino acid having a side chain pK value of greater than 7. Basic amino acids typically have positively charged side chains at physiological pH due to association with hydronium ion. Genetically encoded basic amino acids include His (H), Arg (R) and Lys (K).
[0176] The term "polar amino acid" refers to a hydrophilic amino acid having a side chain that is uncharged at physiological pH, but which has at least one bond in which the pair of electrons shared in common by two atoms is held more closely by one of the atoms. Genetically encoded polar amino acids include Asn (N), Gin (Q) Ser (S) and Thr (T).
[0177] The term "nonpolar amino acid" refers to a hydrophobic amino acid having a side chain that is uncharged at physiological pH and which has bonds in which the pair of electrons shared in common by two atoms is generally held equally by each of the two atoms (i.e., the side chain is not polar). Genetically encoded nonpolar amino acids include Leu (L), Val (V), He (I), Met (M), Gly (G) and Ala (A). [0178] The term "aromatic amino acid" refers to a hydrophobic amino acid with a side chain having at least one aromatic or heteroaromatic ring. In some embodiments, the aromatic or heteroaromatic ring may contain one or more substituents such as— OH,— SH, — CN,— F,—CI,—Br,—I,— N02,—NO,— NH2,— NHR,— NRR,— C(0)R,— C(0)OH, — C(0)OR, — C(0)NH2, — C(0)NHR, — C(0)NRR and the like where each R is independently (Ci - C6) alkyl, substituted (Ci - C6) alkyl, (Ci - C6) alkenyl, substituted (Ci - C6) alkenyl, (Ci - C6) alkynyl, substituted (Ci - C6) alkynyl, (C5 - C20) aryl, substituted (C5 - C2o) aryl, (C6 - C26) alkaryl, substituted (C6 - C26) alkaryl, 5-20 membered heteroaryl, substituted 5-20 membered heteroaryl, 6-26 membered alkheteroaryl or substituted 6-26 membered alkheteroaryl. Genetically encoded aromatic amino acids include Phe (F), Tyr (Y) and Trp (W).
[0179] The term "aliphatic amino acid" refers to a hydrophobic amino acid having an aliphatic hydrocarbon side chain. Genetically encoded aliphatic amino acids include Ala (A), Val (V), Leu (L) and He (I).
[0180] The amino acid residue Cys (C) is unusual in that it can form disulfide bridges with other Cys (C) residues or other sulfanyl-containing amino acids. The ability of Cys (C) residues (and other amino acids with— SH containing side chains) to exist in a peptide in either the reduced free— SH or oxidized disulfide -bridged form affects whether Cys (C) residues contribute net hydrophobic or hydrophilic character to a peptide. While Cys (C) exhibits a hydrophobicity of 0.29 according to the normalized consensus scale of Eisenberg (Eisenberg, 1984, supra), it is to be understood that for purposes of the preferred embodiments Cys (C) is categorized as a polar hydrophilic amino acid, notwithstanding the general classifications defined above.
[0181] As used herein, the term "targeting moiety" refers to a structure that binds or associates with a biological moiety or fragment thereof.
[0182] In some embodiments, the targeting moiety may be a monoclonal antibody (mAB). In some embodiments, the targeting moiety may be an antibody fragment, surrogate, or variant. In some embodiments, the targeting moiety may be a protein ligand. In some embodiments, the targeting moiety may be a protein scaffold. In some embodiments, the targeting moiety may be a peptide. In some embodiments, the targeting moiety may be RNA or DNA. In some embodiments, the targeting moiety may be a RNA or DNA fragment. In some embodiments, the targeting moiety may be a small molecule ligand. [0183] In some embodiments, the targeting moiety may be an antibody fragment described in Janthur et al., "Drug Conjugates Such as Antibody Drug Conjugates (ADCs), Immunotoxins and Immunoliposomes Challenge Daily Clinical Practice," Int. J. Mol. Sci. 2012, 13, 16020-16045, the disclosure of which is incorporated herein by reference in its entirety. In some embodiments, the targeting moiety may be an antibody fragment described in Trail, PA, "Antibody Drug Conjugates as Cancer Therapeutics," Antibodies 2013, 2, 113- 129, the disclosure of which is incorporated herein by reference in its entirety.
[0184] In some embodiments, the targeting moiety may be HuM195-Ac-225, HuM195-Bi-213, Anyara (naptumomab estafenatox; ABR-217620), AS1409, Zevalin (ibritumomab tiuxetan), BIIB015, BT-062, Neuradiab, CDX-1307, CR011-vcMMAE, Trastuzumab-DMl (R3502), Bexxar (tositumomab), IMGN242, IMGN388, IMGN901, 131I- labetuzumab, IMMU-102 (90Y-epratuzumab), IMMU-107 (90Y-clivatuzumab tetraxetan), MDX-1203, CAT-8015, EMD 273063 (hul4.18-IL2), Tucotuzumab celmoleukin (EMD 273066; huKS-IL2), 188Re-PTI-6D2, Cotara, L19-IL2, Teleukin (F16-IL2), Tenarad (F16- 131I), L19-131I, L19-TNF, PSMA-ADC, DI-Leul6-IL2, SAR3419, SGN-35, or CMC544. In some embodiments, the targeting moiety may comprise, consist of, or consist essentially of the antibody portion of HuM195-Ac-225, HuM195-Bi-213, Anyara (naptumomab estafenatox; ABR-217620), AS 1409, Zevalin (ibritumomab tiuxetan), BUBO 15, BT-062, Neuradiab, CDX-1307, CR011-vcMMAE, Trastuzumab-DMl (R3502), Bexxar (tositumomab), IMGN242, IMGN388, IMGN901, 131I-labetuzumab, IMMU-102 (90Y- epratuzumab), IMMU-107 (90Y-clivatuzumab tetraxetan), MDX-1203, CAT-8015, EMD 273063 (hul4.18-IL2), Tucotuzumab celmoleukin (EMD 273066; huKS-IL2), 188Re-PTI- 6D2, Cotara, L19-IL2, Teleukin (F16-IL2), Tenarad (F16-131I), L19-131I, L19-TNF, PSMA- ADC, DI-Leul6-IL2, SAR3419, SGN-35, or CMC544.
[0185] In some embodiments, the targeting moiety may be Brentuximab vedotin, Trastuzumab emtansine, Inotuzumab ozogamicin, Lorvotuzumab mertansine, Glembatumumab vedotin, SAR3419, Moxetumomab pasudotox, Moxetumomab pasudotox, AGS-16M8F, AGS-16M8F, BIIB-015, BT-062, IMGN-388, or IMGN-388.
[0186] In some embodiments, the targeting moiety may comprise, consist of, or consist essentially of the antibody portion of Brentuximab vedotin, Trastuzumab emtansine, Inotuzumab ozogamicin, Lorvotuzumab mertansine, Glembatumumab vedotin, SAR3419, Moxetumomab pasudotox, Moxetumomab pasudotox, AGS-16M8F, AGS-16M8F, BIIB-015, BT-062, IMGN-388, or IMGN-388. [0187] In some embodiments, the targeting moiety may comprise, consist of, or consist essentially of Brentuximab, Inotuzumab, Gemtuzumab, Milatuzumab, Trastuzumab, Glembatumomab, Lorvotuzumab, or Labestuzumab.
[0188] As used herein, the term "linker" refers to a moiety that connects two or more components to each other.
[0189] In some embodiments, the linker may be a linker disclosed in Janthur et al., "Drug Conjugates Such as Antibody Drug Conjugates (ADCs), Immunotoxins and Immunoliposomes Challenge Daily Clinical Practice," Int. J. Mol. Sci. 2012, 13, 16020- 16045. In some embodiments, the linker may be a linker disclosed in Trail, PA, "Antibody Drug Conjugates as Cancer Therapeutics," Antibodies 2013, 2, 113-129. In some embodiments, the linker may be a linker disclosed in US Patent No.: 7,829, 531.
[0190] In some embodiments, the linker may comprise, consist of, or consist essentially of the linker portion of HuM195-Ac-225, HuM195-Bi-213, Anyara (naptumomab estafenatox; ABR-217620), AS 1409, Zevalin (ibritumomab tiuxetan), BUBO 15, BT-062, Neuradiab, CDX-1307, CR011-vcMMAE, Trastuzumab-DMl (R3502), Bexxar (tositumomab), IMGN242, IMGN388, IMGN901, 131I-labetuzumab, IMMU-102 (90Y- epratuzumab), IMMU-107 (90Y-clivatuzumab tetraxetan), MDX-1203, CAT-8015, EMD 273063 (hul4.18-IL2), Tucotuzumab celmoleukin (EMD 273066; huKS-IL2), 188Re-PTI- 6D2, Cotara, L19-IL2, Teleukin (F16-IL2), Tenarad (F16-131I), L19-131I, L19-TNF, PSMA- ADC, DI-Leul6-IL2, SAR3419, SGN-35, or CMC544.
[0191] In some embodiments, the linker may comprise, consist of, or consist essentially of the linker portion of Brentuximab vedotin, Trastuzumab emtansine, Inotuzumab ozogamicin, Lorvotuzumab mertansine, Glembatumumab vedotin, SAR3419, Moxetumomab pasudotox, Moxetumomab pasudotox, AGS-16M8F, AGS-16M8F, BIIB-015, BT-062, IMGN-388, or IMGN-388.
[0192] In some embodiments, the linker may comprise, consist of, or consist essentially of Valine-citrulline residue, hydrazine, 4-mercaptobutanoyl, 4-(N- succinimidomethyl)cyclohexanecarbonyl (SMCC), Maleimidocaproyl, Phenylalaninelysine, 6-(3-(thio)propanamido)hexanoyl, 3-mercaptopropanoyl, 4-mercaptopentanoyl, or lysine residue.
[0193] In some embodiments, the linker may comprise, consist of, or consist essentially of:
Figure imgf000056_0001
wherein L5 may be optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L5 is Ci-Cg alkyl.
[0194] In some embodiments, the linker may comprise, consist of, or consist essentially of:
Figure imgf000056_0002
, wherein A is the targeting moiety, L may be optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L5 is Ci-Cg alkyl.
[0195] In some embodiments, the linker may comprise, consist of, or consist essentially of:
Figure imgf000057_0001
substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted
Ci-Cg alkyl. In some embodiments, L5 is Ci-Cg alkyl. L6 may be H, optionally substituted Ci-
Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof.
[0196] In some embodiments, the linker may comprise, consist of, or consist essentially of:
Figure imgf000057_0002
, wherein A is the targeting moiety, L5 may be optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted C3-C8 cylcoalkyl annulated to cyclooctyl ring, optionally substituted Ci-Cg alkoxy, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or combination thereof. In some embodiments, L5 is an optionally substituted Ci-Cg alkyl. In some embodiments, L5 is Ci-Cg alkyl.
[0197] In some embodiments, the linker may comprise, consist of, or consist essentially of:
Figure imgf000058_0001
-57-
Figure imgf000059_0001
-58-
Figure imgf000060_0001
[0198] As will be appreciated by those of skill in the art, the above-defined categories are not mutually exclusive. Thus, amino acids having side chains exhibiting two or more physical-chemical properties can be included in multiple categories. For example, amino acid side chains having aromatic moieties that are further substituted with polar substituents, such as Tyr (Y), may exhibit both aromatic hydrophobic properties and polar or hydrophilic properties, and can therefore be included in both the aromatic and polar categories. The appropriate categorization of any amino acid will be apparent to those of skill in the art, especially in light of the detailed disclosure provided herein.
[0199] While the above-defined categories have been exemplified in terms of the genetically encoded amino acids, the amino acid substitutions need not be, and in certain embodiments preferably are not, restricted to the genetically encoded amino acids. In some embodiments, the active agent-conjugate may contain genetically non-encoded amino acids. Thus, in addition to the naturally occurring genetically encoded amino acids, amino acid residues in the active agent-conjugate may be substituted with naturally occurring non- encoded amino acids and synthetic amino acids.
[0200] Certain commonly encountered amino acids which provide useful substitutions for the active agent-conjugates include, but are not limited to, β-alanine (β-Ala) and other omega-amino acids such as 3-aminopropionic acid, 2,3-diaminopropionic acid (Dpr), 4-aminobutyric acid and so forth; a-aminoisobutyric acid (Aib); ε-aminohexanoic acid (Aha); δ-aminovaleric acid (Ava); N-methylglycine or sarcosine (MeGly); ornithine (Orn); citrulline (Cit); t-butylalanine (t-BuA); t-butylglycine (t-BuG); N-methylisoleucine (Melle); phenylglycine (Phg); cyclohexylalanine (Cha); norleucine (Nle); naphthylalanine (Nal); 4- phenylphenylalanine, 4-chlorophenylalanine (Phe(4-Cl)); 2-fluorophenylalanine (Phe(2-F)); 3-fluorophenylalanine (Phe(3-F)); 4-fluorophenylalanine (Phe(4-F)); penicillamine (Pen); l,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic); β-2-thienylalanine (Thi); methionine sulfoxide (MSO); homoarginine (hArg); N-acetyl lysine (AcLys); 2,4-diaminobutyric acid (Dbu); 2,3-diaminobutyric acid (Dab); p-aminophenylalanine (Phe (pNH2)); N-methyl valine (MeVal); homocysteine (hCys), homophenylalanine (hPhe) and homoserine (hSer); hydroxyproline (Hyp), homoproline (hPro), N-methylated amino acids and peptoids (N- substituted glycines).
[0201] Other amino acid residues not specifically mentioned herein can be readily categorized based on their observed physical and chemical properties in light of the definitions provided herein.
[0202] The classifications of the genetically encoded and common non-encoded amino acids according to the categories defined above are summarized in Table 2, below. It is to be understood that Table 2 is for illustrative purposes only and does not purport to be an exhaustive list of amino acid residues and derivatives that can be used to substitute the active agent-conjugate described herein.
TABLE 2. CLASSIFICATIONS OF COMMONLY ENCOUNTERED AMINO ACIDS
Classification Genetically Encoded Non-Genetically Encoded
Hydrophobic
Aromatic F, Y, W Phg, Nal, Thi, Tic, Phe (4-Cl), Phe (2-F),
Phe (3-F), Phe (4-F), hPhe
Nonpolar L, V, I, M, G, A, P t-BuA, t-BuG, Melle, Nle, MeVal, Cha,
McGly, Aib
Aliphatic A, V, L, I b-Ala, Dpr, Aib, Ahx, MeGly, t-BuA, t-
BuG, Melle, Cha, Nle, MeVal
Hydrophilic
Acidic D, E
Basic H, Κ, Ρν Dpr, Orn, hArg, Phe(p-NH2), Dbu, Dab
Polar C, Q, N, S. T Cit, AcLys, MSO, bAla, hSer
Helix-Breaking P, G D-Pro and other D-amino acids (in L- peptides)
[0203] Other amino acid residues not specifically mentioned herein can be readily categorized based on their observed physical and chemical properties in light of the definitions provided herein.
[0204] While in most instances, the amino acids of the compound-conjugate will be substituted with L-enantiomeric amino acids, the substitutions are not limited to L- enantiomeric amino acids. In some embodiments, the peptides may advantageously be composed of at least one D-enantiomeric amino acid. Peptides containing such D-amino acids are thought to be more stable to degradation in the oral cavity, gut or serum than are peptides composed exclusively of L-amino acids.
[0205] Examples of compound-conjugates include, but are not limited to, the following general compounds:
Figure imgf000063_0001
R may be H (hydrogen), Ci-Cg alkyl, substituted or cyclic Ci-Cg alkyl
X may be S (sulfur), CH2, CH-OH, CH-OR, CH-ONH2, or C=0.
[0206] Examples of compounds include, but are not limited to, the following general compounds:
Figure imgf000063_0002
Figure imgf000064_0001
-63- [0201] Examples of compound-conjugates include, but are not limited to, the following general compounds:
Figure imgf000065_0001
R may be H (hydrogen), Ci-C8 alkyl, substituted or cyclic Ci-C8 alkyl, and the like
X may be S (sulfur), CH2, CH-OH, CH-OR, CH-ONH2, C=0, and the like.
[0207] Examples of compounds include, but are not limited to, the following compound and general compounds:
Figure imgf000065_0002
Figure imgf000066_0001
Figure imgf000067_0001
Pharmaceutical Compositions
[0208] In some embodiments, the compounds disclosed herein are used in pharmaceutical compositions. The compounds can be used, for example, in pharmaceutical compositions comprising a pharmaceutically acceptable carrier prepared for storage and subsequent administration. Also, embodiments relate to a pharmaceutically effective amount of the products and compounds disclosed above in a pharmaceutically acceptable carrier or diluent. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A.R. Gennaro edit. 1985), which is incorporated herein by reference in its entirety. Preservatives, stabilizers, dyes and even flavoring agents can be provided in the pharmaceutical composition. For example, sodium benzoate, ascorbic acid and esters of p- hydroxybenzoic acid can be added as preservatives. In addition, antioxidants and suspending agents can be used.
[0209] The compositions can be formulated and used as tablets, capsules, or elixirs for oral administration; suppositories for rectal administration; sterile solutions, suspensions for injectable administration; patches for transdermal administration, and sub- dermal deposits and the like. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. Suitable excipients are, for example, water, saline, dextrose, mannitol, lactose, lecithin, albumin, sodium glutamate, cysteine hydrochloride, and the like. In addition, if desired, the injectable pharmaceutical compositions may contain minor amounts of nontoxic auxiliary substances, such as wetting agents, pH buffering agents, and the like. If desired, absorption enhancing preparations (for example, liposomes), can be utilized.
[0210] Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds can be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or other organic oils such as soybean, grapefruit or almond oils, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents that increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
[0211] Pharmaceutical preparations for oral use can be obtained by combining the active compounds with solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents can be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions can be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments can be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses. For this purpose, concentrated sugar solutions can be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments can be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.
[0212] To formulate the compounds of Formulae I and II as an anti-cancer agent, known surface active agents, excipients, smoothing agents, suspension agents and pharmaceutically acceptable film-forming substances and coating assistants, and the like can be used. Preferably alcohols, esters, sulfated aliphatic alcohols, and the like can be used as surface active agents; sucrose, glucose, lactose, starch, crystallized cellulose, mannitol, light anhydrous silicate, magnesium aluminate, magnesium methasilicate aluminate, synthetic aluminum silicate, calcium carbonate, sodium acid carbonate, calcium hydrogen phosphate, calcium carboxymethyl cellulose, and the like can be used as excipients; magnesium stearate, talc, hardened oil and the like can be used as smoothing agents; coconut oil, olive oil, sesame oil, peanut oil, soya can be used as suspension agents or lubricants; cellulose acetate phthalate as a derivative of a carbohydrate such as cellulose or sugar, or methylacetate- methacrylate copolymer as a derivative of polyvinyl can be used as suspension agents; and plasticizers such as ester phthalates and the like can be used as suspension agents. In addition to the foregoing preferred ingredients, sweeteners, fragrances, colorants, preservatives and the like can be added to the administered formulation of the compound produced by the method of the embodiment, particularly when the compound is to be administered orally.
[0213] When used as an anti-cancer compound, for example, the compounds of Formulae I and II or compositions including compounds of Formulae I and II can be administered by either oral or non-oral pathways. When administered orally, it can be administered in capsule, tablet, granule, spray, syrup, or other such form. When administered non-orally, it can be administered as an aqueous suspension, an oily preparation or the like or as a drip, suppository, salve, ointment or the like, when administered via injection, subcutaneously, intraperitoneally, intravenously, intramuscularly, or the like.
[0214] In one embodiment, the anti-cancer agent can be mixed with additional substances to enhance their effectiveness.
Methods of Administration
[0215] In an alternative embodiment, the disclosed compounds and the disclosed pharmaceutical compositions are administered by a particular method as an anti-cancer, or anti-inflammatory. Such methods include, among others, (a) administration though oral pathways, which administration includes administration in capsule, tablet, granule, spray, syrup, or other such forms; (b) administration through non-oral pathways, which administration includes administration as an aqueous suspension, an oily preparation or the like or as a drip, suppository, salve, ointment or the like; administration via injection, subcutaneously, intraperitoneally, intravenously, intramuscularly, intradermally, or the like; as well as (c) administration topically, (d) administration rectally, or (e) administration vaginally, as deemed appropriate by those of skill in the art for bringing the compound of the present embodiment into contact with living tissue; and (f) administration via controlled released formulations, depot formulations, and infusion pump delivery. As further examples of such modes of administration and as further disclosure of modes of administration, disclosed herein are various methods for administration of the disclosed compounds and pharmaceutical compositions including modes of administration through intraocular, intranasal, and intraauricular pathways.
[0216] The pharmaceutically effective amount of the compositions that include the described compounds required as a dose will depend on the route of administration, the type of animal, including human, being treated, and the physical characteristics of the specific animal under consideration. The dose can be tailored to achieve a desired effect, but will depend on such factors as weight, diet, concurrent medication and other factors which those skilled in the medical arts will recognize. In a typical embodiment, a compound represented by Formulae I and II can be administered to a patient in need of an anti-cancer agent, until the need is effectively reduced or preferably removed.
[0217] In practicing the methods of the embodiment, the products or compositions can be used alone or in combination with one another, or in combination with other therapeutic or diagnostic agents. These products can be utilized in vivo, ordinarily in a mammal, preferably in a human, or in vitro. In employing them in vivo, the products or compositions can be administered to the mammal in a variety of ways, including parenterally, intravenously, subcutaneously, intramuscularly, colonically, rectally, vaginally, nasally or intraperitoneally, employing a variety of dosage forms. Such methods may also be applied to testing chemical activity in vivo.
[0218] As will be readily apparent to one skilled in the art, the useful in vivo dosage to be administered and the particular mode of administration will vary depending upon the age, weight and mammalian species treated, the particular compounds employed, and the specific use for which these compounds are employed. The determination of effective dosage levels, that is the dosage levels necessary to achieve the desired result, can be accomplished by one skilled in the art using routine pharmacological methods. Typically, human clinical applications of products are commenced at lower dosage levels, with dosage level being increased until the desired effect is achieved. Alternatively, acceptable in vitro studies can be used to establish useful doses and routes of administration of the compositions identified by the present methods using established pharmacological methods.
[0219] In non-human animal studies, applications of potential products are commenced at higher dosage levels, with dosage being decreased until the desired effect is no longer achieved or adverse side effects disappear. The dosage may range broadly, depending upon the desired affects and the therapeutic indication. Typically, dosages can be between about 10 mg/kg and 100 mg/kg body weight, preferably between about 100 mg/kg and 10 mg/kg body weight. Alternatively dosages can be based and calculated upon the surface area of the patient, as understood by those of skill in the art. Administration is preferably oral on a daily or twice daily basis.
[0220] The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. See for example, Fingl et al. , in The Pharmacological Basis of Therapeutics, 1975, which is incorporated herein by reference in its entirety. It should be noted that the attending physician would know how to and when to terminate, interrupt, or adjust administration due to toxicity, or to organ dysfunctions. Conversely, the attending physician would also know to adjust treatment to higher levels if the clinical response were not adequate (precluding toxicity). The magnitude of an administrated dose in the management of the disorder of interest will vary with the severity of the condition to be treated and to the route of administration. The severity of the condition may, for example, be evaluated, in part, by standard prognostic evaluation methods. Further, the dose and perhaps dose frequency, will also vary according to the age, body weight, and response of the individual patient. A program comparable to that discussed above can be used in veterinary medicine.
[0221] Depending on the specific conditions being treated, such agents can be formulated and administered systemically or locally. A variety of techniques for formulation and administration can be found in Remington's Pharmaceutical Sciences, 18th Ed., Mack Publishing Co., Easton, PA (1990), which is incorporated herein by reference in its entirety. Suitable administration routes may include oral, rectal, transdermal, vaginal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.
[0222] For injection, the agents of the embodiment can be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiological saline buffer. For such transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. Use of pharmaceutically acceptable carriers to formulate the compounds herein disclosed for the practice of the embodiment into dosages suitable for systemic administration is within the scope of the embodiment. With proper choice of carrier and suitable manufacturing practice, the compositions disclosed herein, in particular, those formulated as solutions, can be administered parenterally, such as by intravenous injection. The compounds can be formulated readily using pharmaceutically acceptable carriers well known in the art into dosages suitable for oral administration. Such carriers enable the compounds of the embodiment to be formulated as tablets, pills, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated.
[0223] Agents intended to be administered intracellularly can be administered using techniques well known to those of ordinary skill in the art. For example, such agents can be encapsulated into liposomes, then administered as described above. All molecules present in an aqueous solution at the time of liposome formation are incorporated into the aqueous interior. The liposomal contents are both protected from the external micro- environment and, because liposomes fuse with cell membranes, are efficiently delivered into the cell cytoplasm. Additionally, due to their hydrophobicity, small organic molecules can be directly administered intracellularly.
[0224] Determination of the effective amounts is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. In addition to the active ingredients, these pharmaceutical compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. The preparations formulated for oral administration can be in the form of tablets, dragees, capsules, or solutions. The pharmaceutical compositions can be manufactured in a manner that is itself known, for example, by means of conventional mixing, dissolving, granulating, dragee-making, levitating, emulsifying, encapsulating, entrapping, or lyophilizing processes.
[0225] Compounds disclosed herein can be evaluated for efficacy and toxicity using known methods. For example, the toxicology of a particular compound, or of a subset of the compounds, sharing certain chemical moieties, can be established by determining in vitro toxicity towards a cell line, such as a mammalian, and preferably human, cell line. The results of such studies are often predictive of toxicity in animals, such as mammals, or more specifically, humans. Alternatively, the toxicity of particular compounds in an animal model, such as mice, rats, rabbits, dogs or monkeys, can be determined using known methods. The efficacy of a particular compound can be established using several art recognized methods, such as in vitro methods, animal models, or human clinical trials. Art-recognized in vitro models exist for nearly every class of condition, including the conditions abated by the compounds disclosed herein, including cancer, cardiovascular disease, and various immune dysfunction, and infectious diseases. Similarly, acceptable animal models can be used to establish efficacy of chemicals to treat such conditions. When selecting a model to determine efficacy, the skilled artisan can be guided by the state of the art to choose an appropriate model, dose, and route of administration, and regime. Of course, human clinical trials can also be used to determine the efficacy of a compound in humans.
[0226] As will be understood by one of skill in the art, "need" is not an absolute term and merely implies that the patient can benefit from the treatment of the anti-cancer agent in use. By "patient" what is meant is an organism that can benefit by the use of an anticancer agent.
[0227] "Therapeutically effective amount," "pharmaceutically effective amount," or similar term, means that amount of drug or pharmaceutical agent that will result in a biological or medical response of a cell, tissue, system, animal, or human that is being sought. In a preferred embodiment, the medical response is one sought by a researcher, veterinarian, medical doctor, or other clinician.
[0228] In one embodiment, a described compound, preferably a compound having any one of Formulas I and II, including those as described herein, is considered an effective anti-cancer agent if the compound can influence 10% of the cancer cells, for example. In a more preferred embodiment, the compound is effective if it can influence 10 to 50% of the cancer cells. In an even more preferred embodiment, the compound is effective if it can influence 50-80% of the cancer cells. In an even more preferred embodiment, the compound is effective if it can influence 80-95% of the cancer cells. In an even more preferred embodiment, the compound is effective if it can influence 95-99% of the cancer cells. "Influence" is defined by the mechanism of action for each compound.
EXAMPLES
General synthetic procedures
General procedure A - HATU mediated amide bond formation
[0229] To an acid (1.1 eq with respect to amine) in anhydrous DMF was added HATU (1 eq with respect to acid) and DIEA (2 eq with respect to acid) and the mixture was stirred at room temperature for 1 minute. The mixture was then added to a solution of amine in DMF and the reaction mixture was stirred at room temperature till the completion of the reaction (monitored by LC/MS). The solvent was removed under reduced pressure and the residue was optionally purified by reverse phase HPLC to give final pure product.
General procedure B - DIC/HOAt mediated amide bond formation [0230] To a stirred solution of carboxylic acid (1.1 eq), amine and HO At (1.1 eq) in anhydrous DMF was added DIC (1.1 eq) and the reaction mixture was stirred at room temperature. Upon completion (monitored by LC/MS), the solvent was removed under reduced pressure and the residue was optionally purified by reverse phase HPLC to give final pure product.
General procedure C - Removal of acid sensitive protecting groups (Boc, THP, t-Bu) using HCl/dioxane
[0231] The acid sensitive protecting groups containing compound was dissolved in 4N HCl/dioxane and the mixture was stirred at room temperature for 2 h. The solution was then concentrated under reduced pressure and the residue was washed twice with cold ether. Purification was carried out on reverse phase HPLC if necessary.
General procedure D - Removal of Fmoc group
[0232] The Fmoc containing compound was dissolved in 2-5% piperidine in DMF. The mixture was stirred at room temperature for lh. The solvents were removed under reduced pressure. Purification was carried out on reverse phase HPLC if necessary.
General procedure E - Reductive alkylation
[0233] An amine was dissolved in DMF and aldehyde (5 eq) was added, followed by addition of sodium cyanoborohydride (5 eq). HOAc was added to adjust the pH of the reaction mixture to 4-5. The mixture was stirred at room temperature till completion (1-4 h, monitored by HPLC). Purification was carried out on reverse phase HPLC if necessary.
General procedure F - Saponification - removal of Me/Et from esters
[0234] To a stirred solution of an ester in MeOH was added 1M aq. solution of LiOH till pH of the mixture was about 13-14 and the reaction mixture was stirred at room temperature till completion (~ 16h, monitored by HPLC). Citric acid (-10% aq,) was added to neutralize the reaction and the solvents were removed under reduced pressure. The crude product was optionally purified by RP-HPLC or used directly in the next step.
General procedure G - Activation of a hydroxyl/phenol group with bis(p- nitrophenyOcarbonate
[0235] To a stirred solution of an alcohol/phenol in THF/DMF (2/1) was added bis(p-nitrophenyl) carbonate (3-5 eq), followed by DIEA (2-4 eq) and the reaction mixture was stirred at room temperature until most of the starting material was consumed. The progress of the reaction was monitored by LC/MS. The crude product was optionally purified by flash column chromatography or by precipitation and washing. General procedure H - Reaction of an amine with a cyclic anhydride (glutaric anhydride or succinic anhydride)
[0236] An amine containing compound was dissolved in DMF. Glutaric anhydride (3 eq) was added, followed by addition of DIE A (4 eq). The reaction mixture was stirred at room temperature until most of the starting material was consumed. The progress of the reaction was monitored by LC/MS. The crude product was purified by RP-HPLC to yield the pure carboxylic acid.
General procedure I - Formation of carbamate with p-nitrophenyl carbonate (e.g. FmocVC- PAB-PNP
[0237] An amine containing compound was dissolved in DMF and alkyl/aryl p- nitrophenyl carbonate (1.5 eq) was added, followed by addition of DIEA (2 eq) and HOBt (cat., 5%). The reaction mixture was stirred at room temperature until most of the amine was consumed. The progress of the reaction was monitored by LC/MS. The crude product was optionally purified by RP-HPLC to yield the pure carbamate.
General procedure J - Formation of an activated ester (e.g. NHS) from an acid
[0238] An acid was dissolved in DCM and DMF was added to aid dissolution if necessary. N-hydroxysuccinimide (1.5 eq) was added, followed by EDC.HCl (1.5 eq). The reaction mixture was stirred at room temperature for 1 h until most of the acid was consumed. The progress of the reaction was monitored by RP-HPLC. The mixture was then diluted with DCM and washed successively with citric acid (aq. 10%) and brine. The organic layer was dried and concentrated to dryness. The crude product was optionally purified by RP-HPLC or silica gel column chromatography.
General scheme for active agent conjugates formation
Conjugation method A. Conjugation on Lys residues via an activated carboxylic acid
Figure imgf000075_0001
Conjugation method B. Conjugation on Lys residues via reductive alkylation with an dialdehyde
Figure imgf000075_0002
Conjugation method C. Conjugation on individual Cys side chain employing maleimide chemistry
Figure imgf000076_0001
Conjugation method D. Conjugation on two Cys side chains by forming a cyclic structure
Figure imgf000076_0002
Conjugation method F. Conjugation on azide bearing biologies using copper-free click chemistry:
Figure imgf000076_0003
Experimental Description
Step 1. Drug-Linker construct synthesis (-L2-D)
Methods of Drug-Linker construct synthesis, but not limited to:
Method 1-1: Linker and Drug connected via a carbamate bond. The following general procedures were employed:
General procedure G and I for activation and carbamate formationGeneral procedure C, D, and F for removal of protective groups for further derivatization.
Figure imgf000077_0001
Figure imgf000078_0001
Figure imgf000078_0002
o
Method 1-2: Linker and Drug connected via reductive alkylation (General procedure E)
Figure imgf000078_0003
Method 1-3. Active molecule containing a carboxylic acid moiety connected to an alkoxyamino linker via formation of hydoxamate (General procedure A or B), followed by removal of protective groups.
Figure imgf000079_0001
[0239] For active molecules that are hydoxamic acids, the above method still can be employed since the construct will release hydroxamic acid under enzymatic cleavage conditions. The reaction needs to start from its corresponding carboxylic acid.
Figure imgf000079_0002
Step 2. Introducing functional groups to L1-CL2-D)
Methods to introduce functional groups that suitable for conjugation reaction, but no limited to:
Method 2-1. Compounds bearing free amino group to react with an cyclic anhydride to introduce carboxylic acid (General procedure H).
Figure imgf000080_0001
Method 2-2. Compounds bearing free amino group to react with a di-acid to introduce carboxylic acid (General procedure B).
Figure imgf000080_0002
Method 2-3. Removal of carboxylic acid protective group to reveal the free carboxylic acid
Figure imgf000081_0001
Method 2-4. Reductive alkylation of a primary amine with a dialdehyde bearing a carboxylic acid moiety (General procedure E)
Figure imgf000081_0002
[0240] The amine (NH2-Ahx-Maytansinol) (20 mg) was dissolved in acetonitrile (2 mL) and 1 mL of NaOAc buffer (100 mM, pH = 4.0) was added. The dialdehyde (0.5 M solution in water, 0.2 mL) was added, followed by NaCNBH3 (10 mg). The reaction mixture was stirred at room temperature for 30 mins and purified directly by RP-HPLC to give the desired acid (16 mg) as a white solid after lyophilization. MS found: 790.5 (M+H)+.
[0241] The dialdehyde carboxylic acid was synthesized according to the followin scheme:
Figure imgf000081_0003
[0242] The ester, 2H-Pyran-4-carboxylic acid, 2-ethoxyl-3,4-dihydro-ethyl ester was synthesized according to a literature procedure (Chem Communications, (1) 25-26, 1998) was saponified using General procedure F, followed by treatment with IN aq. HCl at room temperature for lh. The aq. solution of dialdehyde was used directly without further purification.
Metho -5. Introduction of o-phenylenediamine moiety
Figure imgf000082_0001
[0243] The 3-nitro-4-amino benzoic acid was incorporated using standard amidation reaction (General procedure B). The nitro group was reduced using sodium dithionite (3 eq) in acetonitrile/water to give the desired o-phenylene diamine. MS found: 1504.8 (M+H)+.
Step 3. Introducing the final functional groups prior to conjugation
Methods of introduction of final reactive group prior to conjugation reaction, but not limited to:
Method 3-1. Activation of a carboxylic acid to its corresponding activated form
Figure imgf000083_0001
[0244] G is a leaving group selected from -F, -CI,- Br, -I, -N3, -OR (R = alkyl, aryl, heteroaryl, substituted aryl, substituted heteroaryl), SR (R = alkyl, aryl heteroaryl, substituted aryl, substituted heteroaryl), -ON(R1)R2, (R1, R2 are each independently selected from -(C=0)-R, R = H, alkyl, aryl, heteroaryl, substituted aryl, substituted heteroaryl or R1 and R2 are connected to form a cyclic structure, or R1=R2=(=C-R), RC(=0)0-, and RSO2-O- (R = alkyl, aryl, heteroaryl, substituted aryl, substituted heteroaryl).
[0245] The carboxylic acid can be activated using a variety of methods to afford an activated form. For example, the carboxylic acid can be activated using the following methods: A) Tetrahedron 61 (2005) 10827-10852; B) Beckwith, A. L. J. In The Chemistry of
Amides; Zabicky, J., Ed.; Synthesis of Amides; Interscience: London, 1970; pp 105-109; C)
Handbook of Reagents for Organic Synthesis: Activating Agents and Protecting Groups;
Pearson, A. J., Roush, W. R., Eds.; Wiley: New York, 1999; pp 370-373; D) Lloyd-Williams,
P., Albericio, F., and Giralt, E. (1997). Chemical approaches to the synthesis of peptide and proteins (Series ed. C. W. Rees). CRC Press, New York; E) Peptide chemistry: A practical textbook: By M Bodansky. Springer-Verlag, Heidelberg. 1988; and F) The practice of peptide synthesis, 2nd ed., by M. Bodansky and A. Bodansky, Springer-Verlag, New York, each of which is incorporated herein by reference in its entirety.
Method 3-2. Introducing a maleimido moiety
a. Via amidation (General procedure A, or B, or from an activated ester bearing a maleimido moiety)
Figure imgf000084_0001
b. Converting an existing amino group to maleimide directly using N-methoxycarbonylmaleimide
Figure imgf000084_0002
[0246] The amine (0.1 mmol) was dissolved in acetonitrile/water (6/4, v/v, 3 mL). The mixture was cooled in an ice-water bath and treated with sat. aq. NaHC03 (0.5 mL), followed by N-methoxycarbonylmaleimide (0.12 mmol). The mixture was stirred at room temperature for 1 h. The pH was adjusted to 6-7 with citric acid and the solution was concentrated. The residue was purified by RP-HPLC to yield the desired maleimide as a white powder after lyophilization (58%). MS found: 1091.2 (M+H)+.
Method 3-3. Formation of dibromomethyl quinoxaline
Figure imgf000085_0001
[0247] The o-phenylenediamino compound (12 mg) was dissolved in acetonitrile/water. Dibromomethyl diketone (10 mg) was added. The mixture was stirred at room temperature for 10 min and purified directly by RP-HPLC to give the desired quinoxaline as a white powder (12 mg) after lyophilization. MS found 1713.0 (M+H)+.
Method 3-4. Incorporation of hydroxylamine moiety
Figure imgf000086_0001
-85- Example I. Synthesis of compound 10
Figure imgf000087_0001
Scheme I. Reagents and conditions: i. SOCl2, EtOH; ii. DEPC, TFA, DCM; iii. TFA, DCM; iv. BrOP, DCM, DIEA; v. TFA, DCM; iv. DIEA, DCM, HOBt.
[0248] To a solution of compound 1 (23.4g, 81.53mmol) in dry EtOH (200 mL) was added SOCl2 (100 mL) at 0°C. The mixture was stirred for overnight and the solvent was removed by evaporation in vacuo. The residue was immediately used for the next step without further purification. To a solution of compound 2 (81.53 mmol), compound 3 (50 g, 163.1 mmol) in dry DMF (150 mL) was added DEPC (15.9 g, 97.8 mmol), TEA (41 g, 0.408 mol) at 0 °C. The mixture was stirred for 2 h at 0 °C. Then the mixture was stirred overnight at room temperature. Solvent was removed by evaporation in vacuo. The residue was diluted with ethyl acetate-toluene (2: 1, 900 ml) and washed with 1M KHSO4, water, sat. NaHCOs, and brine. The organic layer was dried and concentrated to give a residue, which was purified by column (hexanes: ethyl acetate: DCM= 5: 1 : 1) to give 38g of compound 4.
[0249] To a solution of Boc-Val-OH (30.6 g, 0.142 mol), compound 5 (from 25g of compound 4) in DCM (400 mL) was added BrOP (28 g, 70.87 mmol), DIEA (30 g, 0.236 mol) at 0 °C. The mixture was shielded from light and stirred for 0.5 h at 0 °C. Then the mixture was stirred for 48 h at room temperature. The solvent was removed by evaporation in vacuo. The residue was diluted with ethyl acetate-toluene (3: 1, 900 mL) and washed with 1M KHSO4, water, sat. NaHCC"3, and brine. The organic layer was dried and concentrated to give a residue, which was purified by silica gel column (hexanes: ethyl acetate: DCM= 3: 1 : 1) to give 22 g of compound 7.
[0250] To a solution of compound 7 (40 g, 66.7 mmol) in THF (600 mL) was added a mixture of LiOH (14 g, 0.33 mol) in water (300 mL) below 10 °C. The mixture was stirred for 5 days at 25 °C. THF was removed by evaporation. The aqueous layer was washed with Et20 (200 mL x 3). The aqueous layer was acidified to pH 2 with IN HC1 at 0 °C, the mixture was extracted with ethyl acetate and the organic layer was washed with water and brine. The organic layer was dried and concentrated to give a residue, which was purified by Prep-HPLC to give 14 g of compound 8.
[0251] To a solution of compound 8 (3 g) in DCM (100 mL) was added compound 9 (3 g, prepared according to General procedure J from Boc-N-Me-Val-OH using EDC and pentafluorophenol). DIEA (2.6 mL) was added, followed by HOBt (cat. 100 mg) and the reaction mixture was stirred at room temperature for 16 h. The solvents were removed under reduced pressure and the residue was purified on a silica gel column to give compound 10 as a white powder (3.1 g). . MS m/z Calcd for C35H64N4O9 684.5, Found 707.6 ([M+Na]+).
Exam le II. Pre aration of c totoxic com ounds - sulfonamide derivatives
Figure imgf000088_0001
Figure imgf000089_0001
Figure imgf000090_0001
Figure imgf000091_0001
Example Ila. Synthesis of compound 13, 14, 16, 18.
Figure imgf000092_0001
Figure imgf000092_0002
Scheme Ila. Reagents and conditions: i. DIC/HOAt, DMF, rt, 16 h; ii. HCl/Dioxane
[0252] The amino acid sulfonamide derivatives 11, 15, 17, 19 were synthesized according to previously reported procedure (ARKIVOC 2004 (xii) 14-22) using Boc protected amino acid and cyclopropyl/methyl sulfonamide, followed by removal of Boc
(General procedure C)
Example IIa-1. Synthesis of compound 13
[0253] Compound 13 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 1) and amine 11, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 13 as a white powder after lyophilization. MS m/z Calcd for C42H70N6O9S
834.5, Found 835.6 ([M+H]+).
Example IIa-2. Synthesis of compound 14
[0254] Compound 14 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 10) and amine 15, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase
HPLC to give compound 14 as a white powder after lyophilization. MS m/z Calcd for
C4oH68N609S 808.5, Found 809.6 ([M+H]+).
Example IIa-3. Synthesis of compound 16
[0255] Compound 16 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 10) and amine 17, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase
HPLC to give compound 16 as a white powder after lyophilization. MS m/z Calcd for
C39H72N6O9S 800.5, Found 801.7 ([M+H]+).
Example IIa-4. Synthesis of compound 18
[0256] Compound 18 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 10) and amine 19, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase
HPLC to give compound 18 as a white powder after lyophilization. MS m/z Calcd for
C4iH69N709S 835.5, Found 836.6 ([M+H]+).
Example lib. Synthesis of compound 27
Figure imgf000094_0001
o=s=o
j r26 R = Boc I
Scheme lib. Reagents and conditons: i. compound 11, EDC, HOBt, DMF; ii. HC1, iPrOH; iii. PyBrOP, DIEA, DCM; iv. TFA, DCM; v. Boc20, NaHC03, dioxane, water; vi. HATU, DIEA, DMF.
[0257] To a stirred solution of compound 1 (2.9 g, 10 mmol) and compound 11 (HC1 salt, 3 g) in anhydrous DMF (100 mL) was added HOBt (1.54 g) and EDC.HC1 (2 g). DIEA (20 mmol) was added and the mixture was stirred at room temperature for 16 h. The solvents were removed under reduced pressure and the residue was dissolved in ethyl acetate (500 mL) and washed successively with Citric acid (10%, aq., 200 mL), NaHC03 (sat. aq., 200 mL) and brine. The organic layer wad dried and evaporated to dryness to give compound
20 as a syrup which was treated with 6N HC1 in iPr-OH (100 mL) for 1 h to give compound
21 after concentration. Compound 21 was used directly without further purification.
[0258] To a solution of Boc-Val-OH (2.5 g), compound 22 in DCM (150 mL) was added PyBrOP (11 mmol), DIEA (22) at 0 °C. The mixture was shielded from light and stirred for 0.5 h at 0 °C. Then the mixture was stirred for 24 h at room temperature. The solvent was removed by evaporation in vacuo. The residue was diluted with ethyl acetate (300 mL) and washed with 1M KHSO4, water, sat. NaHC03, and brine. The organic layer was dried and concentrated to give a residue, which was purified by silica gel column (hexanes: ethyl acetate) to give 3.2 g of compound 23.
[0259] The compound 23 (3 g) was dissolved in DCM (100 mL) and TFA (30 mL) was added. The mixture was stirred at room temperature for 2 h and concentrated under reduced pressure. The residue was dissolved in dixoane (200 mL). Sat. aq. NaHC03 (80 mL) was added, followed by Boc anhydride (2.2 g). The mixture was stirred at room temperature for 4 h and neutralized to pH 3- 4 using IN HCl. Solvents were removed and the residue was dissolved in ethyl acetate, which was washed with water and brine. The organic layer was concentrated and the residue was purified on a silica gel column to give compound 25 as a syrup.
[0260] Compound 27 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between compound 21 and amine 25, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 27 as a white powder after lyophilization. MS m/z Calcd. for C36H59N508S 721.4, Found 722.5 ([M+H]+).
Example lie. Synthesis of compounds 30, 31, and 31.
Figure imgf000095_0001
Scheme lie. Reagents and conditions: i. HATU, DIEA, DMF; ii. HCl/dioxane, MeOH
Example IIc-1. Synthesis of compound 30
[0261] Compound 30 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between β-Cl-N-Boc-Ala-OH (compound 28) and amine 27, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 30 as a white powder after lyophilization. MS m/z Calcd for C3 H63CIN6O9S 826.4, Found 827.5 ([M+H]+).
Example lie -2. Synthesis of compound 31
[0262] Compound 31 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between
N-Boc-Aib-OH and amine 27 followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 31 as a white powder after lyophilization. MS m/z Calcd. for C4oH66N609S 806.5, Found 807.8 ([M+H]+).
Example IIc-3. Synthesis of compound 32
[0263] Compound 32 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between
N-Boc-Sar-OH and amine 27, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 32 as a white powder after lyophilization. MS m/z Calcd. for
Figure imgf000096_0001
792.5, Found 793.4 ([M+H]+).
Example lid. Synthesis of compounds 35 and 37.
Figure imgf000096_0002
Scheme lid. Reagents and conditions: i. DIC/HOAt, DMF, rt, 16 h; ii. HCl/Dioxane
[0264] The amino acid sulfonamide derivatives 33 and 36 were synthesized according to previously reported procedure (WO 2007146695) using Boc protected amino acid and cyclopropyl/methyl sulfonamide, followed by removal of Boc (General procedure C)
Example IId-1. Synthesis of compound 35
[0265] Compound 35 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 10) and amine 33, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase HPLC to give compound 35 as a white powder after lyophilization. MS m/z Calcd for
C4iH7oN6OioS 838.5, Found 839.6 ([M+H]+).
Example lid -2. Synthesis of compound 37
[0266] Compound 37 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 10) and amine 36, followed by removal of Boc (General procedure C). The final compound was purified by reverse phase
HPLC to give compound 37 as a white powder after lyophilization. MS m/z Calcd for
C43H72N6OioS 864.5, Found 865.7 ([M+H]+).
Example He. Synthesis of compounds 44 and 45
Figure imgf000097_0001
Scheme He. Reagents and conditions: i. bis(nitrophenyl) carbonate, DIEA, THF/DMF, r.t; ii. 6-aminohexanoic acid, NaHC03 (aq.); iii. HCl/Dixoane (4N); iv. HCHO, NaCNBH3, DMF, HO Ac; v. DIC, HO At, NH2-0-THP; vi. HC1/H20 (4N), DMF.
Example IIe-1. Synthesis of compound 44
[0267] The phenol 35 (lmmol) was treated with 3eq of bis(p- nitrophenyl)carbonate to form the activated carbonate 39 (general procedure G). The crude product was used directly without further purification. 6-Aminohexanoic acid (5eq) was dissolved in sat. aq. NaHC03 (5 mL) and the solution was added. The reaction mixture was stirred at room temperature for 16h. Citric acid (aq. 10%) was added to acidify the reaction
(pH = 4-5) and then diluted with EtOAc (150 mL). Organic layer was dried (over Na2S04) and concentrated to give the crude product 40 which underwent the following procedures: removal of Boc (General procedure C), reductive alkylation using HCHO (General procedure E), DIC/HOAt mediated amide bond formation (General procedure B) between compound 42 and THP-0-NH2, followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 44 as a white powder after lyophilization. MS m/z Calcd for C48H82N8Oi3S 1010.6, Found 1011.8 «M+H]+).
Example IIe-2. Synthesis of compound 45
[0268] The compound 45 was synthesized according to the same procedures as described for the synthesis of compound 44. The final compound was purified by reverse phase HPLC to give compound 45 as a white powder after lyophilization. MS m/z Calcd for
C5oH84N8Oi3S 1036.6, Found 1037.5 ([M+H]+).
Figure imgf000098_0001
Figure imgf000099_0001
Figure imgf000100_0001
Scheme III. Reagents and conditions: i. HATU, DIEA, DMF; ii. HCl/dioxane; iii. HCHO, NaCNBH3, DMF, HOAc; iv. LiOH, MeOH/H20
Example III- 1. Synthesis of compound 49
[0269] Compound 49 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between
Boc-N-Me-Val-Val-Dil-Dap-OH(compound 10) and NH2-Leu-OMe, followed by removal of
Boc (General procedure C), reductive alkylation with HCHO (General procedure E) and saponification to remove methyl group from ester (General procedure F). The final compound was purified by reverse phase HPLC to give compound 49 as a white powder after lyophilization. MS m/z Calcd for CsyHggNsOs 711.5, Found 712.5 ([M+H]+).
Example III -2. Synthesis of compound 50
[0270] Compound 50 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between
Boc -N-Me-Val-Val-Dil-Dap-OH(compound 10) and amine 51, followed by removal of Boc (General procedure C), reductive alkylation with HCHO (General procedure E) and saponification to remove methyl group from ester (General procedure F). The final compound was purified by reverse phase HPLC to give compound 51 as a white powder after lyophilization. MS m/z Calcd for CsgHyiNjOs 737.5, Found 738.5 ([M+H]+).
Compound 51 was synthesized according to literature procedures (J. Org. Chem., 2001 , 66, 7355-7364)
Example III -3. Synthesis of compound 52
[0271] Compound 52 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between
Boc-N-Me-Val-Val-Dil-Dap-OH(compound 1) and amine 22, followed by removal of Boc and t-Bu (General procedure C), reductive alkylation with HCHO (General procedure E). The final compound was purified by reverse phase HPLC to give compound 52 as a white powder after lyophilization. MS m/z Calcd for C4iH66N508 783.6, Found 784.7 ([M+H]+).
Example III -4. Other compounds synthesized using the same procedures as described for the synthesis of compound 49
[0272] For compound 53: MS m/z Calcd for QsHysNjOs 787.6, Found 788.7
«M+H]+).
[0273] For compound 54: MS m/z Calcd for C42H69N508 771.5 Found 772.5 +).
Figure imgf000101_0001
Example I
Figure imgf000102_0001
Scheme III-5. Reagents and conditions: i. HATU, DIEA DMF, rt, 1 h; ii. HCl/Dioxane, MeOH; iii. phenylboronic acid, hexanes, water, rt, 18 h.
Example III-5a. Synthesis of compound 137
[0274] The intermediate 136 was synthesized using the general procedures described above as following (0.1 mmol scale): HATU mediated amide bond formation
(General procedure A) between Boc-N-Me-Val-Val-Dil-Dap-OH (compound 1) and amine
134, followed by removal of Boc (General procedure C). The HC1 salt 11 was dissolved in water (5 mL) and hexane (5 mL) was added. Phenylboronic acid (10 eq) was added and the suspension was stirred vigorously at room temperature for 1 h. Hexane layer was removed and fresh hexane (5 mL) was added. The mixture was agitated for another 2 h and the aqueous layer was collect and concentrated. The final compound was purified by reverse phase HPLC to give compound 12 as a white powder after lyophilization. MS m/z Calcd for
C34H64BN508 681.5, Found 682.4 ([M+H]+).
Example III-5b. Synthesis of compound 138
[0275] The compound 138 was synthesized employing the same sequence as described for the preparation of compound 137. (compound 139 as a starting material). It was obtained as a white powder after RP-HPLC purification and lyophilization. MS m/z Calcd for
C35H68BN508 697.5, Found 698.6 ([M+H]+). Exam le IV. Pre aration of c totoxic com ounds - h droxamic acid derivatives
Figure imgf000103_0001
Figure imgf000104_0001
Scheme IV. Reagents and conditions: i. DIC/HOAt, DMF; ii. HCl/water, DMF
Example IV- 1. Synthesis of compound 56
[0276] Compound 56 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Me2-Val-Val-Dil-Dap-LeuOH (compound 49) and THP-0-NH2, followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 56 as a white powder after lyophilization. MS m/z
Calcd for CsyHyoNeOs 726.5, Found 727.6 ([M+H]+).
Example IV-2. Synthesis of compound 57
[0277] Dimethyl Auristatin F was synthesized from compound 10 and NH2-Phe-
OMe using the synthetic procedures described above for the synthesis of compound 49.
[0278] Compound 57 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between dimethyl auristatin F and THP-0-NH2, followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 57 as a white powder after lyophilization. MS m/z Calcd for C4oH68N608
760.5, Found 761.6 ([M+H]+). Example IV-3. Synthesis of compound 58
[0279] Compound 58 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Tubulysin (J. Am. Chem. Soc, 2006, 128 (50), pp 16018-16019) and THP-0-NH2, followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 45 as a white powder after lyophilization. MS m/z Calcd for C38H58N607S 742.4, Found 743.5 ([M+H]+).
Example IV-4. Synthesis of compound 59
[0280] Compound 59 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between HTI-286 (Bioorg Med Chem Lett. 2004, 14(16):4329-32) and THP-0-NH2, followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 59 as a white powder after lyophilization.
MS m/z Calcd for C27H44N404488.3, Found 489.5 ([M+H]+).
Example IV-5. Synthesis of compound 60
[0281] Compound 60 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 50 and THP-0-NH2, followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 47 as a white powder after lyophilization. MS m/z Calcd for C39H72N608 752.5,
Found 753.5 ([M+H]+).
Example IV-6. Synthesis of compound 61
[0282] Compound 61 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 52 and THP-0-NH2, followed by removal of THP (General procedure C, using 4N aq. HCl). The final compound was purified by reverse phase HPLC to give compound 61 as a white powder after lyophilization. MS m/z Calcd for C4iH78N609 798.5,
Found 799.5 ([M+H]+). Example V. Synthesis of alkoxyamine linkers 65, 66, 67, and 68.
Figure imgf000107_0002
Figure imgf000107_0001
Fmoc'
66 -N H^
Scheme V. Reagents and conditions: i. SOCl2, THF, lh; ii. N-hydroxyphthalimide, NaHC03, DMF, rt, 48 h; iii. NH2NH2.H20, HOAc, DMF.
Example V-l . Synthesis of compound 65
[0283] To a stirred solution of Fmoc-VA-PAB (62) (Bioconjugate Chem., 2002,
13, 855-859) (9 g, 15 mmol) in THF (200 mL) was added thionyl chloride (18 mmol) dropwise. After the addition was complete, the reaction mixture was stirred at room temperature for lh. TLC analysis (ethyl acetate/hexane, 1/1, v/v) showed the completion of the reaction. The solvents were removed under reduced pressure and the residue was washed with hexanes (100 mL) to give compound 63 as a slightly yellowish solid (8.8 g).
[0284] Compound 63 (6.2 g, 10 mmol) was dissolved in anhydrous DMF (100 mL). N-Hydroxy-phthalimide (3.2 g, 20 mmol) was added, followed by solid NaHC03 (3.4 g, 40 mmol). The reaction mixture was stirred at room temperature for 48 h. TLC analysis showed that most of compound 61 was consumed. The reaction was then diluted with ethyl acetate (500 mL) and washed successively with sat. aq. NaHC03 (3 x 200 mL) and brine (200 mL). The organic layer was dried and concentrated to give compound 64 as a tan solid, which was used directly without further purification.
[0285] The crude compound 64 from previous step was dissolved in DMF (100 mL). HO Ac (6 mL) was added, followed by hydrazine hydrate (5 mL). The reaction was stirred at room temperature for lh. LC/MS showed the completion of the reaction. The reaction mixture was then poured into a beaker containing 1L of water under stirring. The precipitated solid was collected via filtration and washed twice with water to give compound
65 as a white solid (purity > 85%, can be used directly). Pure compound 63 was obtained after RP-HPLC purification. MS m/z Calcd for C3oH34N405 530.3, Found 531.4 ([M+H]+).
Example V-2. Synthesis of compound 66
[0286] Compound 66 was synthesized starting from compound Fmoc-VC-PAB
(Bioconjugate Chem., 2002, 13, 855-859) using the procedures described above for the synthesis of compound 63. MS m/z Calcd for C33H40N6O6616.3, Found 617.5 ([M+H]+).
Example V-3. Synthesis of compound 67
[0287] Compound 64 was synthesized starting from compound Fmoc-A-PAB
(synthesized according to the procedure reported: Bioconjugate Chem., 2002, 13, 855-859) using the procedures described above for the synthesis of compound 63. MS m/z Calcd for
C25H25N304431.2, Found 432.6 ([M+H]+).
Example V-4. Synthesis of compound 68
[0288] Compound 68 was synthesized starting from compound Fmoc-Ahx-PAB using the procedures described above for the synthesis of compound 68. MS m/z Calcd for
C28H3iN304473.2, Found 474.3 ([M+H]+).
Figure imgf000109_0001
Figure imgf000110_0001
Scheme 11. Reagents and conditions: i. DIC, HO At, DMF, r.t.; ii. Piperidine, DMF; iii. Glutaric anhydride, DIEA, DMF, rt.
Example VIII- 1. Synthesis of compound 83
[0289] Compound 83 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Auristatin F and compound 65, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 83 as a white powder after lyophilization.
MS m/z Calcd for CeoHgsNgOis 1149.7, Found 1150.9 ([M+H]+).
Figure imgf000112_0001
Figure imgf000112_0002
Figure imgf000112_0003
Example VIII -2 Synthesis of compound 84
[0290] Compound 84 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Auristatin F and compound 66, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 84 as a white powder after lyophilization.
MS m/z Calcd for C63Hioi i iOi4 1235.8, Found 1237.1 ([M+H]+).
Example VIII -3. Synthesis of compound 85
[0291] Compound 85 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Auristatin F and compound 67, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 85 as a white powder after lyophilization.
MS m/z Calcd for CssHseNsOiz 1050.6, Found 1051.9 ([M+H]+).
-I l l- Example VIII -4. Synthesis of compound 86
[0292] Compound 86 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Auristatin F and compound 68, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 86 as a white powder after lyophilization.
MS m/z Calcd for
Figure imgf000113_0001
1092.7, Found 1093.9 ([M+H]+).
Example VIII -5. Synthesis of compound 88
Figure imgf000113_0002
[0293] Compound 88 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 49 and compound 67, followed by removal of Fmoc (General procedure
D), and amide formation with acid 87 using HATU (General procedure A, 3 eq of acid 87 and 1 eq of HATU were used). The final compound was purified by reverse phase HPLC to give compound 88 as a white powder after lyophilization. MS m/z Calcd for C55H94N8O14
1090.7, Found 1091.9 ([M+H]+).
Example VIII -6. Synthesis of compound 89
[0294] Compound 89 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 50 and compound 67, followed by removal of Fmoc (General procedure
D), and amide formation with acid 87 using HATU (General procedure A, 3eq of acid 87 and
1 eq of HATU were used). The final compound was purified by reverse phase HPLC to give compound 89 as a white powder after lyophilization. MS m/z Calcd for C59H96N8014
1116.7, Found 1118.0 ([M+H]+).
Example VIII -7. Synthesis of compound 90
[0295] Compound 90 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 54 and compound 66, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 90 as a white powder after lyophilization.
+).
Figure imgf000114_0001
Example VIII -8. Synthesis of compound 91
[0296] Compound 91 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 52 and compound 66, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 91 as a white powder after lyophilization.
MS m/z Calcd for C64HI I INI IOI5 1273.8, Found 1274.8 ([M+H]+). Example VIII -9. Synthesis of compound 92
[0297] Compound 92 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between Tubulysin M and compound 66, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 92 as a white powder after lyophilization.
MS m/z Calcd for C6iH9iNiiOi3S 1217.7, Found 1218.9 ([M+H]+).
Example VIII -10. Synthesis of compound 93
[0298] Compound 93 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 53 and compound 66, followed by removal of Fmoc (General procedure
D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 93 as a white powder after lyophilization.
+).
Figure imgf000115_0001
Example VIII -11. Synthesis of compound 94
[0299] Compound 94 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound HTI-286 and compound 66, followed by removal of Fmoc (General procedure D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 94 as a white powder after lyophilization. MS m/z Calcd for C47H71N7O9 877.5, Found 878.4 ([M+H]+). Example IX Synthesis of-Ll-(L2-D)-
Figure imgf000116_0001
Figure imgf000117_0001
Figure imgf000118_0001
Example IX- 1. S
Figure imgf000118_0002
F VC PAB PNP
Figure imgf000118_0003
Scheme IX. Reagents and conditions: i. DIEA, HOBt (5%), DMF, rt, 48 h; ii. Piperidine, DMF; iii. glutaric anhydride, DIEA, DMF
[0300] Compound 97 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 13 and
Fmoc-VC-PAB-PNP, followed by removal of Fmoc (General procedure D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 97 as a white powder after lyophilization. MS m/z Calcd for
CeeHiosNiiOivS 1353.7, Found 1354.9 ([M+H]+).
Example IX-2. Synthesis of compound 98
[0301] Compound 98 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 4 and Fmoc-A-PAB-PNP, followed by removal of Fmoc (General procedure D), and amide formation with acid 87 using HATU (General procedure A, 3eq of acid 87 and 1 eq of HATU were used). The final compound was purified by reverse phase HPLC to give compound 98 as a white powder after lyophilization. MS m/z Calcd for C61H94N8O17S 1242.7, Found 1243.8 ([M+H]+).
Example IX-3. Synthesis of compound 99
Figure imgf000119_0001
100
[0302] Compound 99 was synthesized using the general procedures described above as following: reaction of compound 13 and aldehyde 100 under reductive alkylation conditions (General procedure E) and Fmoc-A-PAB-PNP, followed by removal of t-Bu ester (General procedure C). The final compound was purified by reverse phase HPLC to give compound 99 as a white powder after lyophilization. MS m/z Calcd for C4 H82N6O13S 994.6, Found 995.8 ([M+H]+). Example IX -4 Synthesis of compound 102
Figure imgf000120_0001
[0303] Compound 102 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 16 and Fmoc-A-PAB-PNP, followed by removal of Fmoc (General procedure D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 102 as a white powder after lyophilization. MS m/z Calcd for C55H9oN8Oi5S 1134.6, Found 1135.6 ([M+H]+).
Example IX -5 Synthesis of compound 103
Figure imgf000120_0002
[0304] Compound 103 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 16 and Fmoc-A-PAB-PNP, followed by removal of Fmoc (General procedure D), and amide formation with acid 87 using HATU (General procedure A, 3 eq of acid 87 and 1 eq of HATU were used). The final compound was purified by reverse phase HPLC to give compound 103 as a white powder after lyophilization. MS m/z Calcd for CssHgeNgOnS 1208.7, Found 1209.8 ([M+H]+).
Example IX -6. Synthesis of compound 104
[0305] Compound 104 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 42 and compound 66, followed by removal of Fmoc (General procedure D), and reaction with glutaric anhydride (General procedure H). The final compound was purified by reverse phase HPLC to give compound 104 as a white powder after lyophilization. MS m/z Calcd for C71H115N13O19S 1485.8, Found 1486.9 ([M+H]+).
Example IX-7. Synthesis of compound 105
Figure imgf000121_0001
[0306] Compound 105 was synthesized in the same manner as described for the synthesis of compound 104. The final compound was purified by reverse phase HPLC to give compound 105 as a white powder after lyophilization. MS m/z Calcd for C73H117N13O19S 1511.8, Found 1512.9 ([M+H]+).
Example IX-8. Synthesis of compound 110
Figure imgf000122_0001
Scheme IX-8. Reagents and conditions: i. bis(nitrophenyl) carbonate, DIEA, THF/DMF, r.t.; ii. Piperidine 4-carboxylic acid, NaHC03 (aq.); iii. HCl/Dixoane (4N); iv. HCHO, NaCNBH3, DMF, HOAc.
[0307] The phenol 106 (lmmol) was treated with 3eq of bis(p- nitrophenyl)carbonate to form the activated carbonate 107 (general procedure G). The crude product was used directly without further purification. Piperidine 4-carboxylic acid (5eq) was dissolved in sat. aq. NaHC03 (5 mL) and the solution was added. The reaction mixture was stirred at room temperature for 8h. Citric acid (aq. 10%) was added to acidify the reaction
(pH = 4-5) and then diluted with EtOAc (150 mL). Organic layer was dried (over Na2S04) and concentrated to give the crude product 108 which underwent the following procedures: removal of Boc (General procedure C), and reductive alkylation using HCHO (General procedure E). The final compound was purified by reverse phase HPLC to give compound
110 as a white powder after lyophilization. MS m/z Calcd for C5oH8iN7Oi3S 1019.6, Found
1020.8 ([M+H]+). Example IX-9. Synthesis of compound 113
Figure imgf000123_0001
Scheme X. Reagents and conditions: i. t-Butylbromoacetate, K2CO3, DMF, rt, 2h; ii. HCl/dioxane (4N); iii. HCHO, NaCNBH3, HO Ac, DMF
[0308] To a stirred solution of compound 106 (0.2 mmol, 190 mg) in anhydrous
DMF (5 mL) was added t-butyl bromoacetate (0.3 mmol), followed by solid potassium carbonate (55 mg, 0.4 mmol). The reaction mixture was stirred at room temperature for 2 h.
LC/MS confirmed that the completion of the reaction. The mixture was diluted with EtOAc
(100 mL) and washed with 10% aq. Citric acid and brine. The organic layer was dried and concentrated to dryness to give the crude compound 111, which underwent the following procedures: removal of Boc and t-Bu (General procedure C), and reductive alkylation using
HCHO (General procedure E). The final compound was purified by reverse phase HPLC to give compound 113 as a white powder after lyophilization. MS m/z Calcd for C45H74N6O12S,
922.5 Found 923.7 ([M+H]+).
Example IX-10. Synthesis of compound 114
Figure imgf000123_0002
[0309] Compound 114 was synthesized using the general procedures described above as following: HATU mediated amide bond formation (General procedure A) between compound 113 and methyl isonipecotate, followed by saponification to remove methyl group from ester (General procedure F). The final compound was purified by reverse phase HPLC to give compound 114 as a white powder after lyophilization. MS m/z Calcd for CsiHssNyOisS 1033.6, Found 1034.7 ([M+H]+).
Example IX- 11. Synthesis of compound 115
Figure imgf000124_0001
[0310] Compound 115 was synthesized using the general procedures described above as following: DIC/HOAt mediated amide bond formation (General procedure B) between compound 113 and compound 67, followed by removal of Fmoc (General procedure D), HATU mediated amidation reaction with acid 116 (General procedure A), and saponification to remove methyl group from ester (General procedure F).. The final compound was purified by reverse phase HPLC to give compound 115 as a white powder after lyophilization. MS m/z Calcd for CesHioo ioOnS 1324.7, Found 1325.9 ([M+H]+).
Figure imgf000124_0002
Figure imgf000125_0001
Example X-l. Synthesis of compound 101
Figure imgf000125_0002
[0311] Compound 101 was synthesized using the general procedures described above as following: Carbamate formation (General procedure I) between compound 13 and FmocVC-PAB-PNP, followed by removal of Fmoc (General procedure D), and amidation reaction with 6-maleimidohexanoic acid (General procedure A). The final compound was purified by reverse phase HPLC to give compound 101 as a white powder after lyophilization. MS m/z Calcd for C71H108N12O17S 1432.8, Found 1433.9 ([M+H]+). Example X-2. Converting an existing amino group to maleimide directly using N-methoxycarbonylmaleimide
Figure imgf000126_0001
[0312] The amine (117, 0.1 mmol) was dissolved in acetonitrile/water (6/4, v/v, 3 mL). The mixture was cooled in an ice-water bath and treated with sat. aq. NaHC03 (0.5 mL), followed by N-methoxycarbonylmaleimide (0.12 mmol). The mixture was stirred at room temperature for 1 h. The pH was adjusted to 6-7 with citric acid and the solution was concentrated. The residue was purified by RP-HPLC to yield the desired maleimide 118 as a white powder after lyophilization (58%). MS found: 1091.2 (M+H)+.
Example X-3. Formation of dibromomethyl quinoxaline
[0313] The o-phenylenediamino compound 119 (12 mg) was dissolved in acetonitrile/water (6/4, v/v, 1 mL). NaOAc buffer (100 mM, pH = 4.0, 0.3 mL) was added, followed by addition of dibromomethyl diketone (10 mg). The mixture was stirred at room temperature for 10 min and purified directly by RP-HPLC to give the desired quinoxaline 120 as a white powder (12 mg) after lyophilization. MS found 1829.5 (M+H)+.
Example X-4. Synthesis of compound 136
Figure imgf000128_0001
[0314] Compound 13 (50 mg) was treated with aldehyde under reductive alkylation conditions (General procedure E). Without any purification, hydrazine hydrate (20 μί) was added to the reaction mixture. After 10 min, the crude mixture was purified by RP- HPLC to give compound 136 as a white powder (46 mg). MS found 1026.6 (M+H)+.
Example X-5. Synthesis of compound 139
Figure imgf000129_0001
[0315] Compound 139 was synthesized from compound 137 and carbonate 138 according to General procedure I. MS found: 1 184.8 (M+H)+.
[0316] The Antibody Drug Conjugates depicted in the Figures were prepared according to Example XI.
Example XI. Preparation of Antibody Drug Conjugate
[0317] To a solution of 0.5-50 mgs/mL of Trastuzumab in buffet at pH 6.0-9.0 with 0-30% organic solvent, was added 0.1-10 eq of carboxylic acid activated derivatives of compounds 84, 92, 93, or 98 in a portion wise or continuous flow manner. The reaction was performed at 0-40 °C for 0.5-50 hours with gentle stirring or shaking, monitored by HIC-
HPLC (Hydrophobic Interaction Chromatography-HPLC). The resultant crude ADC product underwent necessary down- stream steps of desalt, buffet changes/formulation, and optionally, purification, using the state-of-art procedures. The final ADC product was characterized by
HIC-HPLC, SEC, RP-HPLC, and optionally LC-MS. The average DAR (drug antibody ratio) was calculated by UV absorption and/or MS spectroscopy.
Example XII. In vitro cytotoxicity experiment
[0318] The cell lines used were SK-BR-3 human breast adenocarcinoma (HER2 triple positive), HCC1954 human Ductal Carcinoma (HER2 triple positive), MCF7 human breast adenocarcinoma (HER2 normal), and MDA-MB-468 human breast adenocarcinoma
(HER2 negative). These cells were available from ATCC. SK-BR-3 cells were grown in McCoy's 5 A medium (Caisson Labs, North Logan, UT) supplemented with 10% fetal bovine serum. HCC1954 cells were grown in RPMI-1640 medium (Caisson Labs, North Logan, UT) supplemented with 10% fetal bovine serum. MCF7 and MDA-MB-468 cells were grown in DMEM/F12 medium (Caisson Labs, North Logan, UT) supplemented with 10% fetal bovine serum. SK-BR-3, MCF7, and MDA-MB-468 cells were plated in 96-well plates at approximately 7,500 cells/well, and HCC1954 cells were plated in 96-well plates at approximately 20,000 cells/well. Compounds or the antibody-drug conjugates were added in duplicates in the same day. After 72 hour incubation at 37°C, CellTiter-Glo (Promega, Madison, WI) were added and cell viability was determined as describe by the manufacture's protocol. The percent viability was determined as following:
% Viability = Average Luminescence Value of the duplicates (treated wells) /
Average Luminescence Value of the untreated wells

Claims

WHAT IS CLAIMED IS:
1. A compound havin the structure of Formula I:
Figure imgf000131_0001
or a pharmaceutically acceptable salt thereof,
wherein:
A is a tubulin binding moiety;
B is an functional moiety; and
are each independently selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl, or optionally R1 and R2 together with the nitrogen to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R1 and R3 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7- membered ring, or optionally R7 and R8 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R1 is R1A or R1B;
R1A comprises a targeting moiety;
R1B is -L1(CH2)nRc, -L10(CH2)nRc or -(CH2)nRc;
R is Ci-Cg alkyl, C3-C8 cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R , or optionally R comprises a targeting moiety;
each RD is independently selected from the group consisting of -OH, -N3, halo, cyano, nitro, -(CH2)nNRERF, -(CH2)nC(=0)NRERF, — 0(CH2)nNRERF, -0(CH2)nC(=0)NRERF, -0(CH2)mOC(=0)NRERF, -NRGC(=0)RH, -NRGS(0)zRH, -0(CH2)mO(CH2)mRJ, -0(CH2)nC(=0)RJ, -0(CH2)nRJ, optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, and optionally substituted -0-(d-C8 alkyl);
each NRERF is independently selected, wherein RE and RF are each independently selected from hydrogen, -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]- [L1(C(R2A)2)r(NR2A)s(C(R2A)2)r]s-(L1)s-RJ,
Figure imgf000132_0001
(L1)s[(C(R2A)2)rO(C(R2A)2)r(L2)s]s-(L1)s-RJ, optionally substituted Ci_8 alkyl, optionally substituted C3-8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each R is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally substituted heterocyclyl;
each RH is independently hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or -NRERF;
each RJ is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)nOR2B, -0(CH2)nOR2B, — (CH2)nNR2BR2B, -C(R2A)2NR2BR2B, -(CH2)nC(=0)OR2B, and -C(=0)NHR2B;
each R2A is independently selected, wherein R2A is selected from the group consisting of hydrogen, halo, -OH, optionally substituted Ci-Cg alkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)nOR2B, -(CH2)nNR2CR2C, -C(=0)OR2B, -C(=0)NR2CR2C, or optionally two geminal R2A and the carbon to which they are attached are together an optionally substituted three- to six-membered carbocyclic ring;
each R2B is independently selected from the group consisting of hydrogen, -OH, -(CH2)„C(=0)OH, -C(=0)(C(R2D)2)„L3R2E, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each NR R is independently selected, wherein each R is independently selected from the group consisting of hydrogen, -OH, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, or optionally both R together with the nitrogen to which they are attached are an optionally substituted heterocyclyl; each R is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each R2E is independently selected from the group consisting of optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, and -(CH2)nC(=0)OR2F;
each R2F is independently selected from the group consisting hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L1 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0- -C(=0)NR2A- -S(=0)NR2A- -S(=0)2NR2A- -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each L2 is independently selected from the group consisting of optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L3 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0- -C(=0)NR2A- -S(=0)NR2A-, -S(=0)2NR2A-, -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each m independently is 1 or 2;
each n independently is 0, 1, 2, 3, 4, 5, or 6;
each r independently is 0, 1, 2, 3, 4, 5, or 6;
each s independently is 0 or 1 ; and
each z independently is 1 or 2
R7 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
R 8 is selected from the group consisting of H (hydrogen), -(CH2)„R C , optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl; and R is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl.
2. The compound of Claim 1 ,
wherein:
A is a fragment selected from the group consisting of:
Figure imgf000134_0001
where Y is CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR, where R is optionally substituted Ci-C8 alkyl, and Z is -F, -SR, -N3, -NR , - ONHR, -OAc, or -OR, where each R is independently H, Ci-Cg alkyl or substituted Ci-Cg alkyl.
3. The compound of any of the preceding Claims,
wherein:
B is an functional moiety selected from: CN, CHO, CH2OH, CH2F, CH2CN, CH2N3, COOH, CO-N(R)OR, CO-N(R)CO-R, CO-CO-NHR, CO-N(R)-S02R, (CH2)pCOOH, (CH2)p-CH(OH)-COOH, CO-(CH2)p-COOH, CH=CH-COOH, CO- CH=CH-COOH, CH=CH-CONHOH, CH=CH-CONH-S02R, CO-CH=CH- CONHOH, B(OH)2, (CH2)p-B(OH)2, PO(OH)2, or (CH2)p-PO(OH)2, -R-COOH, -R- CO-N(R)OR, -R-CO-NHR, -R-CO-N(R)-S02R, where each occurrence of R is independently selected from H (hydrogen), Ci-Cg alkyl, C3-Cg cycloalkyl, substituted Ci-Cg alkyl, substituted C3-Cg cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, and NRERF, and p is 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10.
4. A compound having the structure of Formula IV:
Figure imgf000134_0002
or a pharmaceutically acceptable salt thereof,
wherein: R*-R8 are each independently selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted Ci-Cg alkoxy, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl, or optionally R1 and R2 together with the nitrogen to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R1 and R3 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring, or optionally R7 and R8 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7- membered ring, or optionally R1 is R1A or R1B;
R1A comprises a targeting moiety;
R1B is -L1(CH2)nRc, -L10(CH2)nRc or -(CH2)nRc;
R is Ci-Cg alkyl, C3-Cg cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R , or optionally R comprises a targeting moiety;
each RD is independently selected from the group consisting of -OH, -N3, halo, cyano, nitro, -(CH2)nNRERF, -(CH2)nC(=0)NRERF, — 0(CH2)nNRERF, -0(CH2)nC(=0)NRERF, -0(CH2)mOC(=0)NRERF, -NRGC(=0)RH, -NRGS(0)zRH, -0(CH2)mO(CH2)mRJ, -0(CH2)nC(=0)RJ, -0(CH2)nRJ, optionally substituted Ci-Cg alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, and optionally substituted -0-(d-C8 alkyl);
each NRERF is independently selected, wherein RE and RF are each independently selected from hydrogen, -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]- [L1(C(R2A)2)r(NR2A)s(C(R2A)2)r]s-(L1)s-RJ, -[(L^CCCR^CNR^MQR2^),.]- (L1)s[(C(R2A)2)rO(C(R2A)2)r(L2)s]s-(L1)s-RJ, optionally substituted C1-8 alkyl, optionally substituted C3_8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each R is independently hydrogen, optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally substituted heterocyclyl;
each RH is independently hydrogen, optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or -NRERF; each R is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)„OR2B, -0(CH2)„OR2B, — (CH2)nNR2BR2B, -C(R2A)2NR2BR2B, -(CH2)nC(=0)OR2B, and -C(=0)NHR2B;
each R2A is independently selected, wherein R2A is selected from the group consisting of hydrogen, halo, -OH, optionally substituted Ci-Cg alkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, -(CH2)nOR2B, -(CH2)nNR2CR2C, -C(=0)OR2B, -C(=0)NR2CR2C, or optionally two geminal R2A and the carbon to which they are attached are together an optionally substituted three- to six-membered carbocyclic ring;
each R2B is independently selected from the group consisting of hydrogen, -OH, -(CH2)„C(=0)OH, -C(=0)(C(R2D)2)„L3R2E, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each NR R is independently selected, wherein each R is independently selected from the group consisting of hydrogen, -OH, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-Cg alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, or optionally both R together with the nitrogen to which they are attached are an optionally substituted heterocyclyl;
each R2D is independently selected from the group consisting of hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted -0-(Ci-C8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each R2E is independently selected from the group consisting of optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, and -(CH2)nC(=0)OR2F;
each R2F is independently selected from the group consisting hydrogen, optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L1 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0-, -C(=0)NR2A-, -S(=0)NR2A-, -S(=0)2NR2A-, -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each L2 is independently selected from the group consisting of optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;
each L3 is independently selected from the group consisting of -C(=0)-, -S(=0)-, -C(=S)-, -S(=0)2- -C(=0)0- -C(=0)NR2A- -S(=0)NR2A-, -S(=0)2NR2A- -C(=0)NR2AC(=0)-, and -C(CF3)2NR2A-;
each m independently is 1 or 2;
each n independently is 0, 1, 2, 3, 4, 5, or 6;
each r independently is 0, 1, 2, 3, 4, 5, or 6;
each s independently is 0 or 1 ; and
each z independently is 1 or 2
R7 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
R 8 is selected from the group consisting of H (hydrogen), -(CH2)„R C , optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heterocyclyl;
E is selected from the roup consisting of:
Figure imgf000137_0001
where Y is CH2, S, S=0, C=0, CHF, CHCN, CHN3 CH-OH, CH-ONH2, or CHOR14, where R14 is optionally substituted C C8 alkyl, and Z is -F, -SR14, -N3, - NR14R14, -ONHR14, -OAc, or -OR14, where each R14 is independently H (hydrogen), Ci-Cs alkyl substituted Ci-C8 alkyl, or NRERF;
are each independently selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted Ci-Cg alkoxy, optionally substituted C3-C8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl; and
J is selected from: CN, CHO, CH2OH, CH2F, CH2CN, CH2N3, COOH, CO- N(R15)OR15, CO-N(R15)CO-R15, CO-CO-NHR15, CO-N(R15)-S02R15, (CH2)pCOOH, (CH2)p-CH(OH)-COOH, CO-(CH2)p-COOH, CH=CH-COOH, CO- CH=CH-COOH, CH=CH-CONHOH, CH=CH-CONH-S02R, CO-CH=CH- CONHOH, B(OH)2, (CH2)p-B(OH)2, PO(OH)2, or (CH2)p-PO(OH)2, -R15-COOH, - CO-N(R15)OR15, -CO-N(R15)OR15, -R15-CO-N(R15)OR15, -R15-CO-NHR15, -R15-CO- N(R15)-S02R15, where each occurrence of R15 is independently selected from H (hydrogen), Ci-Cg alkyl, C3-Cg cycloalkyl, substituted Ci-Cg alkyl, substituted C3-Cg cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl and NRERF, and p is 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10.
5. The compound of any one of the preceding Claims,
wherein:
R1 is selected from the group consisting of H (hydrogen), optionally substituted Ci-Cg alkyl, optionally substituted C3-Cg cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl.
6. The compound of any one of the preceding Claims, wherein R1 is H (hydrogen) or optionally substituted Ci-C6 alkyl.
7. The compound of any one of the preceding Claims, wherein R1 is R1A.
8. The compound of Claim 6, wherein R1A comprises a targeting moiety selected from the group consisting of brentuximab, inotuzumab, gemtuzumab, milatuzumab, trastuzumab, glembatumomab, lorvotuzumab, or labestuzumab, or derivatives thereof.
9. The compound of any one of the preceding Claims, wherein R1A further comprises a linker.
10. The compound of any one of Claims 1-6, wherein R1 is R1B.
1 1. The compound of Claim 10, wherein R1B is -C(=0)(CH2)nRc or Rc.
12. The compound of Claim 1 1 , wherein R is Ci-Cg alkyl substituted with one or more RD.
13. The compound of Claim 12, wherein RD is -0(CH2)mOC(=0)NRERF, -0(CH2)mO(CH2)mRJ, or optionally substituted heterocyclyl.
14. The compound of Claim 13, wherein RJ is -C(=0)OR2B; and R2B is -OH.
15. The compound of Claim 11, wherein R is Ci-C8 alkyl substituted with one or more RD.
16. The compound of Claim 12, wherein RD is -0(CH2)mOC(=0)NRERF, -0(CH2)mO(CH2)mRJ, or optionally substituted heterocyclyl.
17. The compound of Claim 13, wherein RJ is -C(=0)OR2B; and R2B is hydrogen.
18. The compound of Claim 10, wherein R1B is -C(=0)0(CH2)„Rc
19. The compound of Claim 18, wherein R is aryl substituted with one or more
RD.
20. The compound of Claim 19, wherein RD is -(CH2)nNRERF; RE is hydrogen; and RF is -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]-[L^C(R2A)2)r(NR2A)s(C(R2A)2)r]s-(L1)s-R^
21. The compound of Claim 20, wherein RF is -[C(=0)(C(R2A)2)(NR2A)]- [L1(C(R2A)2)r]-RJ or -[C(=0)(C(R2A)2)(NR2A)]-L1[(C(R2A)2)rO(C(R2A)2)r]-RJ.
22. The compound of Claim 21 , wherein RJ is -(CH2)nOR2B, or -C(=0)OR2B.
23. The compound of Claim 22, wherein RB is hydrogen or -(CH2)„C(=0)OH.
1
24. The compound of any one of Claims 4-10, wherein R is aryl substituted with one or more RD.
25. The compound of Claim 24, wherein RD is -(CH2)nNRERF; RE is hydrogen; and RF is -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]-[L1(C(R2A)2)r(NR2A)s(C(R2A)2)r]s-(L1)s-RJ.
26. The compound of Claim 25, wherein RF is -[C(=0)(C(R2A)2)(NR2A)]- [C(=0)(C(R2A)2)r(NR2A)]-C(=0)-RJ.
27. The compound of Claim 24, wherein RD is -(CH2)nNRERF; RE is hydrogen; and RF is -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]-(L1)s-RJ.
28. The compound of Claim 27, wherein RF is -[C(=0)(C(R2A)2)r(NR2A)]-C(=0)-
RJ
29. The compound of any one of Claims 25-28, wherein RJ is -(CH2)„C(=0)OR2B; and RB is hydrogen.
30. The compound of Claim 27, wherein RF is -[C(=0)(C(R2A)2)r(NR2A)]-C(=0)-
RJ
31. The compound of Claim 25, wherein RF is -[C(=0)(C(R2A)2)(NR2A)]- C(=0)[(C(R2A)2)rO(C(R2A)2)r]-RJ.
32. The compound of Claim 31, wherein RJ is -0(CH2)„C(=0)OR2B; and RB is hydrogen.
33. The compound of any one of Claims 1-10, wherein R 8 -(CH2)„R C .
34. The compound of Claim 18, wherein Rc is aryl substituted with one or more
RD
35. The compound of Claim 34, wherein RD is -0(CH2)„RJ or -0(CH2)nC(=0)NRERF.
36. The compound of Claim 35, wherein RJ is -(CH2)nC(=0)OR2B; and RB is hydrogen.
37. The compound of Claim 35, wherein RJ is optionally substituted heterocyclyl.
38. The compound of Claim 35, wherein RD is -0(CH2)nC(=0)NRERF; RE is hydrogen; and RF is -[(L1)s(C(R2A)2)r(NR2A)s(C(R2A)2)r]-(L1)s[(C(R2A)2)rO(C(R2A)2)r(L2)s]s-
39. The compound of Claim 38, wherein RF is -0(L2)s-NR2AC(=0)-RJ; and L2 is optionally substituted aryl.
40. The compound of Claim 39, wherein RF is -0(C(R2A)2)(L2)s-(L1)s-RJ.
41. The compound of Claim 40, wherein RF is -0(CH2)(L2)NHC(=0)-RJ; and L2 is optionally substituted aryl.
42. The compound of any one of Claims 39-41, wherein RJ is -C(R2A)2NR2BR2B; each R2A is independently hydrogen or optionally substituted Ci-Cg alkyl; and each R2B is independently hydrogen or -C(=0)(C(R2D)2)nL3R2E.
43. The compound of Claim 42, wherein each R2D is hydrogen; L3 is -C(=0)- or -NR2AC(=0)-; and R2E is optionally substituted heterocyclyl or optionally substituted Ci-C8 alkyl.
44. The compound of any one of the preceding Claims, wherein Rc comprises a targeting moiety; and further comprises a linker.
45. The compound of any one of the preceding Claims having the structure of Formula II:
Figure imgf000140_0001
(II),
a pharmaceutically acceptable salt thereof. wherein:
R9 is selected from the group consisting of H (hydrogen), optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, substituted Ci-C8 alkyl, substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally R7, R8 and R9 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring; and
X is a group consisting of at least one heteroatom.
46. The compound of Claim 45 wherein X is selected from groups consisting of - OR10, -S02-R10, where R10 is Rc
47. The com ound of Claims 1 - 44 having the structure of Formula III:
Figure imgf000141_0001
(in),
or a pharmaceutically acceptable salt thereof;
wherein:
wherein:
R9 is selected from the group consisting of H (hydrogen), optionally substituted Ci-C8 alkyl, optionally substituted C3-C8 cycloalkyl, substituted Ci-C8 alkyl, substituted C3-C8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally R7, R8 and R9 together with the atoms to which they are attached are an optionally substituted cyclic 5- to 7-membered ring,
X is a group consisting of at least one heteroatom;
n is 0 or 1
48. The compound of Claim 47 wherein X is selected from groups consisting of - OR10, -S02-R10, where R10 is Rc.
49. The compound of Claims 45-48, wherein at least one of R1, R8 and X comprises a targeting moiety.
50. The compound of Claim 49, wherein at least one of R1, R8 and X further comprises a linker.
51. The compound of any one of Claims 49 - 50, wherein at least one of R1, R8 and X comprises -(CH2)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
52. The compound of any one of Claims 49 - 50, wherein at least one of R1, R8 and X comprises -(CH2CH20)n- where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
53. The compound of any one of Claims 49 - 50, wherein at least one of R1, R8 and X comprises Val-Cit-PAB, Val-Ala-PAB, Val-Lys(Ac)-PAB, Phe-Lys-PAB, Phe- Lys(Ac)-PAB, D-Val-Leu-Lys, Gly-Gly-Arg, Ala-Ala-Asn-PAB, Ala-PAB, or PAB
54. The compound of any one of Claims 49 - 50, wherein at least one of R1, R8 and X comprises a peptide, oligosaccharide, -(CH2)„-, -(CH2CH20)n-, Val-Cit-PAB, Val-Ala- PAB, Val-Lys(Ac)-PAB, Phe-Lys-PAB, Phe-Lys(Ac)-PAB, D-Val-Leu-Lys, Gly-Gly-Arg, Ala-Ala-Asn-PAB, Ala-PAB, PAB, or combinations thereof.
55. The compound of any one of Claims 49 - 50, wherein the targeting moiety is a monoclonal antibody (mAB).
56. The compound of any one of Claims 49 - 50, wherein the targeting moiety is an antibody fragment, surrogate, or variant.
57. The compound of any one of Claims 49 - 50, wherein the targeting moiety is a protein ligand.
58. The compound of any one of Claims 49 - 50, wherein the targeting moiety is a protein scaffold.
59. The compound of any one of Claims 49 - 50, wherein the targeting moiety is a peptide.
60. The compound of any one of Claims 49 - 50, wherein the targeting moiety is a small molecule ligand.
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