92 players in the nature (Earth) 26 main players in biological systems What are the roles of these guys?

16 Bioinorganic and Environmental Chemistry Key roles of metal ions in biology

Metal Ions Roles Na+, K+ charge carriers, osmotic and electrochemical balance across cell membranes Mg2+, Ca2+ enzyme activators, act as structure promoters and Lewis acids. Fe, Cu, Mo redox (electron-transfer) proteins and enzymes involving Fe(III)/Fe(II), Cu(II)/Cu(I), Mo(VI)/Mo(V)/Mo(IV). Oxygen carrying proteins of iron and copper. Nitrogen fixation by Fe/Mo (V) containing nitrogenase enzymes Zn structure promoter, Lewis acid : Bioinorganic Chemistry - Interdisciplinary subject

Bioinorg.

Chem Spectrocopy Basics – Characteristics of life

살아있는 기관의 특성

• 구조적으로 복잡하고, 고도로 정리 조직되어 있다. • 주위 환경으로부터 에너지를 추출, 변환, 사용한다. • 정밀하게 자기 복제와 자기 조립하는 능력을 가지고 있다.

생명 현상의 분자적 논리 • 다양한 기관들은 공통의 화학적 특성을 갖는다. • 같은 구조적 기본 단위를 가지고 있다.(세포) • 같은 종류의 고분자를 가지고 있다.(DNA, RNA, 단백질) • 고분자들은 같은 종류의 단분자 단위로 만들어져 있다.(nucleotide, amino acid) Basics – Cell

The players of life

단백질(protein) 탄수화물 핵산(nucleaic acids)

The playground Basics – Proteins Basics – Proteins

일차 구조(primary structure): 단백질 사슬의 아미노산 순서

이차 구조(secondary structure): 단 백질 안의 부분적 구조로서 아미노 산이 규칙으로 배열되어 있는 인 a-helix 와 b-sheet 등의 구조

삼차 구조(tertiary structure): 단백질의 전체 모양

사차 구조(quaternary structure): 여러 단백질의 집합체 Basics – Nucleic acids

DNA (deoxyribonucleic acid): 유전 정보를 저장, 전달. 단백질 합성(RNA와 함께)에 관여 (분자량 = 수백만) RNA (ribonucleic acid): 단백질 합성에 관여 (분자량 = 20,000 ~ 40,000) 핵산의 단위체: 뉴클레오타이드(nucleotide) 1. Deoxyribose for DNA and ribose for RNA 2. N을 포함하는 유기 염기

3. 인산(H3PO4)

Ribose (a pentose) Basics – Nucleic acids Polymerization

뉴클레오타이드 의 형성

nucleoside

nucleotide

OH Dimerization OH O P OH Base O P OH O CH Base 2 O O CH2 H H O H H H H O H H H H OH O H H2O

O P OH O P OH Base Base O CH2 O CH2 O O H H H H

H H H H OH H OH H Basics – Nucleic acids (DNA)

A-DNA B-DNA Z-DNA

DNA Basics – Nucleic acids (RNA)

mRNA rRNA tRNA snRNA siRNA miRNA rasiRNA piwiRNA Metal ions in metalloenzymes Porphyrin and related

porphine metalloporphyrine

chlorin corrin Porphyrin and related – Heme

metalloporphyrine Hemeproteins

Oxygen transport – hemoglobin, myoglobin, neuroglobin, cytoglobin, leghemoglobin Catalysis - cytochrome P450s, cytochrome c oxidase, ligninases, peroxidases Electron transfer/transport - cyctochrome a, cytochrome b, cytochrome c Defense -catalase heme

Cytochrome c Porphyrin and related – Chlorin, Corrin

chlorin

corrin Chlorophyll a

Coenzye B12 (Vitamin B12) Porphyrin and related – Hemoglobin, Myoglobn

heme

Hemoglobin (a2b2) Myoglobin [oxygen transport] [oxygen storage] Porphyrin and related – Hemoglobin, Myoglobn

O2 binding to heme (structure and spin)

high spin Fe(II) low spin Fe(II) Porphyrin and related – Hemoglobin, Myoglobn

O2 binding to hemoglobin (corperative)

Hb + O2 ←← HbO2 K1 = 5 to 60

← HbO + O Hb(O ) ←

2 2 ← 2 2 Mb + O2 ← MbO2

Hb(O2)2 + O2 ←← Hb(O2)3 Hb(O2)3 + O2 ←← Hb(O2)4 K4 = 3000 to 6000

D. E. Benson, Wayne State University Porphyrin and related – Hemoglobin, Myoglobn

O2 binding to hemoglobin (allosteric, Bohr effect)

Relation of hemoglobin's oxygen binding affinity – acidity and carbon dioxide concentration ←← - + CO2 + 2H2O → HCO3 + H3O

pH ↑ Porphyrin and related – Catalases

Catalase (a4)

2 H2O2 → 2 H2O + O2

Proposed mechanism J. AM. CHEM. SOC. 2009, 131, 11751–11761 .+ H2O2 + Fe(III)-E → H2O + O=Fe(IV)-E( ) .+ H2O2 + O=Fe(IV)-E( ) → H2O + Fe(III)-E + O2 Porphyrin and related – Peroxidases

Glutathione peroxidase Haloperoxidase Myeloperoxidase (MPO) Catalase Thyroid peroxidase Vanadium bromoperoxidase Lactoperoxidase

H2O2 + 2SH → 2 H2O + 2S

Reaction cycle of peroxidase. (a) Classical peroxidase chemistry. (b) Oxygen-transfer rection. S represents the substrate Porphyrin and related – Peroxidases

Glutathione peroxidase Haloperoxidase Myeloperoxidase (MPO) Catalase Thyroid peroxidase Vanadium bromoperoxidase Lactoperoxidase

H2O2 + 2SH → 2 H2O + 2S Porphyrin and related – Cytochromes

Membrane-bound (i.e. inner mitochondrial membrane) hemeproteins containing heme groups. Primarily responsible for the generation of ATP via electron transport.

- + Cytochrome a – heme a R-H + O2 + 2e + 2H  R-OH + H2O Cytochrome b – heme b Cytochrome c

Cytochrome P450 – strong absorption at 450 nm detoxification in liver :

Human Cytochrome P450 2E1

Chem. Rev. 2004, 104, 3947-3980 Porphyrin and related – Chlorophylls

chlorin

Where is chlorophylls ? Chlorophyll a Chlorophyll b ….. Porphyrin and related – Photosystems

Chloroplast

Chloroplast ultrastructure: 1. outer membrane 2. intermembrane space 3. inner membrane (1+2+3: envelope) 4. stroma (aqueous fluid) 5. thylakoid lumen (inside of thylakoid) 6. thylakoid membrane 7. granum (stack of thylakoids) 8. thylakoid (lamella) 9. starch 10. ribosome 11. plastidial DNA 12. plastoglobule (drop of lipids) Porphyrin and related – Photosystems

Chloroplast

Chlorophylls Porphyrin and related – Photosystems

thylakoid membrane

Photosystem II

Photosystem I Porphyrin and related – Photosystems

Z-Scheme

+ + 2 H2O + 2 NADP + 3 ADP + 3 Pi + light → 2 NADPH + 2 H + 3 ATP + O2 Porphyrin and related – Coenzyme B12

corrin Other Fe Proteins - Ferredoxins ([Fe-S] proteins)

acidic, low molecular weight, soluble iron-sulfur proteins found in various organisms, and act as multifunctional electron carriers in diverse redox systems

Rieske FeS

HiPiP Fds Low-potential Fds Other Fe Proteins – Ferritin

Ferritin: intracellular iron-storage protein Transferrin: transports iron through the blood to the – up to 4,500 Fe atoms liver, spleen and bone marrow.

two specific high-affinity Fe(III) binding sites

a24

Storage: Fe3+ forms Removal: reduction to Fe2+ and chelation Zn Proteins – Carboxypetidase

hydrolyzes a peptide bond at the carboxy-terminal (C-terminal) end of a protein or peptide Cu Proteins

Type-1 Type-2 • “normal copper protein” • tetragonal Cu(II) • “blue copper protein” • less intense than T1 • electron transfer • 600 nm: Cu(II) d-d transition • catalysis Cu Proteins

CuB

CuZ

Type-3 Type-4 (T2/T3) CuA

Mixed-valence Cu(II)-Cu(I) in oxidized state • reversible binding of O2 • Oxy form: Cu(II)-Cu(II) Cu Proteins - Ceruloplasmin

• copper-carrying protein in the blood, and in addition plays a role in iron metabolism • carries more than 95% of the total copper in healthy human plasma

a2 T4 copper center Cu Proteins – Cu, Zn SOD

• Superoxide dismutase Cu Proteins – Cu, Zn SOD

• Superoxide dismutase

Ni-SOD

Mn-SOD Fe-SOD Cu Proteins – Cu, Zn SOD Nitrogen Cycle

N2

NO + NH4 / NH3

- NO2

Organic N

- NO3 Nitrogen Cycle - Nitrogenase

+ - R-homocitrate N2 + 8H + 8e + 16ATP 3 7 → 2NH3 + H2 + 16ADP + 16 Pi 2 6 Fe1 X Mo a-275Cys 4 5 a-442His Nitrogen Cycle - Nitrogenase

N

N

M

NH

N

D M A 1

NH2 NH

N NH

M M

3 NH2 NH3 N NH

M M

NH2

NH NH2

M M NH2 5 M NH3

NH3

M

NH3 Nitrogen Cycle – Nitrite Reductase

Cu-containing Nitrite reductase - NO2 → NO → N2O → N2 Fe-containing Nitrite reductase

Cu-containing Nitrite reductase

a3 Nitrogen Cycle – Nitrite Reductase

Cu-containing Nitrite reductase T2/T1

T2 Nitrogen Cycle – Nitrite Reductase

Cu-containing Nitrite reductase

Proposed mechanism - NO2 → NO Nitrogen Cycle – Nitrite Reductase

Cytochrome cd1 Nitrite reductase

Heme b

a2 Containing c-type cytochrome (for electron transfer)

and d1-type cytochrome (for substrate reduction)

Heme c Heme d1 Nitrogen Cycle – Nitrite Reductase

Cytochrome cd1 Nitrite reductase

Proposed mechanism - NO2 → NO

Dalton Trans. , 2005, 3410–3418 Nitrogen Cycle – Nitrite Reductase

Cytochrome c Nitrite reductase

a2 Containing 5 c-type hemes (per a)

Proposed mechanism - + NO2 + 6e- + 7H → NH3 + 2H2O NO – NO Synthase

inducible NOS (iNOS) endothelial NOS (eNOS) constitutive NOS NOS (cNOS) neural NOS (nNOS)

iNOS NO – NO Synthase

NOS reactions

Schematic structure of the active site of NHA-bound murine iNOS. NHA is shown in bold.

H4B (Tetrahydrobiopterin)

Current Opinion in Chemical Biology 2000, 4:687–695 NO – NO Synthase

Proposed nucleophilic hydroperoxoFe(III)heme mechanism for the NOS-catalyzed oxidation of N-hydroxyarginine. PPIX, protoporphyrin IX Current Opinion in Chemical Biology 2000, 4:687–695 NO – NO Synthase

Proposed radical-type autoxidation mechansim of the NOS- catalyzed oxidation of NHA. Ellipses denote the heme group. P, peroxyFe(III)heme intermediate.

Current Opinion in Chemical Biology 2000, 4:687–695 Metals in Medicine – History

2500 BC : Au, Ag in medical potion 15-16 C : Hg to treat syphilis 18 C : Bi for dyspepsia

1890 : Observation of the bactericidal action of gold cyanide, K[Au(CN)2] 1910 - 20 : Arsenic, bismuth compounds were used to treat syphilis 1930s : Gold drugs were used to treat rheumatoid arthritis 1964 : Barnett Rosenberg discovered the anticancer activity of cisplatin 99m - 1971 : Radiopharmaceutical technetium compound [ TeO4] 1979 : Auranofin for arthritis 1984 : Gd[DTPA]2- for MRI contrast agent 1993 : 153Sm-EDTMP for bond pain

Current medical practice Therapeutic : gold drugs (rheumatoid arthritis), lithium (depression), platinum (cancer), bismuth (stomach ulcers), vanadium (diabetes), iron (anaemia, blood pressure), cobalt (pernicious anaemia)… Diagnostic : imaging applications, In addition to technetium, radioactive forms of thallium, gallium and indium are also used routinely for diagnostic imaging purposes. Metals in Medicine – Cisplatin and related

NH 3 NH 3

Cl Pt NH 3 Cl Pt Cl

Cl NH 3 cisplatin transplatin

Action

1. Hydrolysis of cisplatin

Cl- concentration

In blood, 100 mM In cell, 3 mM Metals in Medicine – Cisplatin and related

Action

2. Cisplatin binding to DNA 3. Kink of DNA 4. HMG binding to DNA

5. Cell death

excision repair cell lives Metals in Medicine – Cisplatin and related

NH3 O Pt NH H N O 3 2 C Structure Activity Relationships (SAR) Pt anticancer compounds satisfyingO SAR O Pt N C O H2 O O O Oxaliplatin CBDCA; Carboplatin

O C H2N O O Pt Cl O NH IV C H3N Pt Cl O NH2 C C O C 1. A cis geometry is required with the general O O DWA 2114R JM216 formula cis-[PtX2(amine)2] for Pt(II), and for Pt(IV) the formula cis-[PtX2Y2 (amine)2]. Monofunctional binding cationic complexes are inactive.

2. The X ligands (leaving groups) should be of - 2- intermediate strength (Cl , SO4 , carboxylate ligands). For Pt(IV) complexes the Y ligands should have a trans orientation and can be Cl-, OH-, or - [O(CO)CnH2n+1] . Pt anticancer compounds violating SAR

O

H2N Cl N NH Cl O O Cl Pt 3. The non-leaving group amine ligands Pt Pt H2N N Cl NH O O N Cl should contain at least one NH moiety, O necessary for hydrogen-bonding interactions with DNA (H-bonding to the O6 of guanine and to the 5’ phosphate group). Metals in Medicine – Non-Pt anticancer complexes Metals in Medicine – Bleomycin

Anticancer activity by induction of DNA strand cleavage. DNA cleavage by bleomycin depends on oxygen and metal ions. Metals in Medicine – Antiarthritic drugs

Metal complexes as cysteine protease inhibitors (PCT/US1996/015527) Harry B Gray, Mark W Grinstaff, Thomas J Meade Study of DNA using Inorganic Agents

Chemistry study - DNA is too big to be directly studied in molecular level.

Breaking DNA (or RNA) to be investigated

Binding to specific sites of DNA and using Fenton reaction

+ 1-(p-bromoacetamidobenzyl)-EDTA Fe(II) [Cu(phen)2]

n+ (n+1)+ - • M + H2O2 → M + OH + OH Study of DNA using Inorganic Agents

hn

3+ D-[Ru(en)2(phi)] Phi = phenanthrenequinone diimine