Medicinal chemistry: drug classes and SAR

Pharmacy (B.Pharm) · Pharmaceutical chemistry and analysis · free study notes for exams, placements and interviews

In short

Medicinal chemistry studies how a drug's chemical structure decides its biological action, and structure-activity relationship (SAR) is the systematic study of what happens to activity when that structure is altered piece by piece. It explains why penicillin G is acid-labile but ampicillin is not, why sulphanilamide needs a free para-amino group, and why propranolol blocks β-receptors while isoprenaline stimulates them. It is a core paper in B.Pharm under the PCI credit-based syllabus (Medicinal Chemistry I-III), carries heavy weight in GPAT, NIPER-JEE and GATE-PH, and is the standard technical round for R&D, formulation development, analytical development and medical-writing jobs at Sun Pharma, Cipla, Dr Reddy's, Lupin, Zydus, Torrent, Glenmark, Aurobindo and CROs such as Syngene, Jubilant Biosys and Sai Life. On the job it drives lead optimisation, impurity and degradation prediction, salt/prodrug selection and justification of pharmacopoeial structural tests.

Explained

Core concepts: pharmacophore, drug-receptor interaction and physicochemical parameters

Pharmacophore: the minimum three-dimensional arrangement of functional groups essential for activity (for morphine: aromatic ring, quaternary-like basic nitrogen two carbons from the ring, phenolic OH, and a specific stereochemistry).
Auxophore (non-essential part): groups that modify potency, duration or absorption without being essential.
Binding forces, in descending strength: covalent (aspirin acetylating COX serine, β-lactams acylating transpeptidase), ionic/electrostatic, ion-dipole and dipole-dipole, hydrogen bonding, charge transfer, van der Waals, hydrophobic. Most drug action is reversible and non-covalent.
Lipophilicity: log P = log(C octanol/C water); for a nominated pH, log D (distribution coefficient) is used. Optimum log P for oral absorption ≈ 1-3; for CNS entry ≈ 2.
Ionisation: by Henderson-Hasselbalch, only the unionised fraction crosses membranes passively; weak acids (aspirin, pKa 3.5) absorb partly from the stomach, weak bases (chloroquine, pKa 8.1/10.2) from the intestine.
Electronic effects: Hammett σ constants quantify how ring substituents withdraw/donate electrons; steric effects via Taft Es or molar refractivity (MR).
Hydrogen-bond count, molecular weight, polar surface area decide permeability; Lipinski's rule of five (MW ≤ 500, log P ≤ 5, H-bond donors ≤ 5, acceptors ≤ 10) flags poor oral prospects; Veber adds rotatable bonds ≤ 10 and TPSA ≤ 140 Å².
Stereochemistry: (S)-(−)-propranolol is ~100× more active than (R); levofloxacin is the active (S)-enantiomer of ofloxacin; (R)-thalidomide is sedative while (S) is teratogenic. Eudismic ratio = activity of eutomer/distomer.

How SAR is studied, and the tools of lead optimisation

Identify the lead (natural product, screening hit, by-product of clinical observation, me-too design).
Dissect the molecule: vary one feature at a time - substituent, chain length, ring size, stereochemistry, functional group - and plot activity.
Homologation: activity usually rises along a homologous series to an optimum then falls (alkyl chain of n-alkyl resorcinols; C5-C6 peak).
Chain branching and ring-chain transformation usually lower activity by worsening fit.
Isosterism/bioisosterism (Erlenmeyer, Friedman): replacement by groups of similar size/electronic character, giving similar (classical) or antagonistic action.
- Classical: −F for −H, −O− for −S− or −NH−, −COOH for −SO₂NH₂ or tetrazole (losartan), −Cl for −CF₃.
- Non-classical: ring equivalents, amide ↔ ester ↔ sulphonamide, carbonyl ↔ sulphone.
Prodrug design: a bio-reversible derivative made for better absorption (enalapril → enalaprilat), taste masking (chloramphenicol palmitate), site specificity (sulfasalazine for the colon), longer action (fluphenazine decanoate), or water solubility (fosphenytoin). Soft drugs are the reverse - designed to break down predictably after acting.
Molecular hybridisation, rigidification and conformational restriction to raise selectivity.
QSAR: mathematical correlation of activity with physicochemical descriptors - Hansch (linear free energy, uses log P, π, σ, Es), Free-Wilson (de novo additivity of substituent contributions), and 3D-QSAR (CoMFA). Validated by r², q² (cross-validated), s and F.

Major drug classes and their SAR - chemotherapeutic agents

Sulphonamides (sulphanilamide nucleus): essential features - free aromatic −NH₂ at N4 (or a group convertible to it in vivo, as in prontosil), the −SO₂NH− bridge, para relationship of the two nitrogens, and an unsubstituted/monosubstituted N1. N1-heteroaryl substitution (sulphamethoxazole, sulphadiazine) lowers pKa towards 6-7.5, raising potency; N4-substitution abolishes activity. Mechanism: competitive antagonism of PABA at dihydropteroate synthase; synergistic with trimethoprim (DHFR inhibitor) - sequential blockade in co-trimoxazole.
β-Lactam antibiotics: the strained, non-planar fused β-lactam ring is essential - it acylates transpeptidase (PBP). SAR: an electron-withdrawing acyl side chain (phenoxymethyl in penicillin V) confers acid stability; an α-amino group (ampicillin, amoxicillin) gives Gram-negative reach and oral activity; bulky ortho-disubstituted aryl (methicillin, cloxacillin) resists staphylococcal penicillinase; free 3-COOH needed for binding; opening the ring (penicilloic acid) or amide hydrolysis destroys activity. Cephalosporins (7-ACA) tolerate C7 and C3 variation - generations 1 to 5 trade Gram-positive for Gram-negative and β-lactamase stability. Clavulanic acid, sulbactam and tazobactam are suicide inhibitors of β-lactamase.
Quinolones: 4-oxo-3-carboxylic acid (both essential for DNA gyrase/topoisomerase IV binding), N1-alkyl/cyclopropyl, 6-F boosts potency ~30×, C7-piperazine broadens the spectrum, C8 affects phototoxicity. Chelates with Fe²⁺, Ca²⁺, Al³⁺ and Mg²⁺ - hence the antacid/milk interaction.
Antitubercular: isoniazid (a prodrug activated by mycobacterial KatG; free hydrazide essential), pyrazinamide (nicotinamide bioisostere), ethambutol (only the (S,S)-isomer active), rifampicin (semi-synthetic rifamycin). Fixed-dose combinations are supplied under the National TB Elimination Programme.
Antimalarials: 4-aminoquinolines (chloroquine - 7-Cl and the basic diaminoalkyl side chain of 4 carbons between the two nitrogens for optimal potency), 8-aminoquinoline (primaquine - tissue schizonticide, hazard in G6PD deficiency), artemisinin's endoperoxide bridge is the pharmacophore - ACT is the national first-line therapy for P. falciparum - artesunate + sulfadoxine-pyrimethamine in most of India, artemether-lumefantrine in the north-eastern states.
Anticancer: alkylating agents (nitrogen mustards - cyclophosphamide is a prodrug activated by CYP2B6), antimetabolites (methotrexate as a folate analogue; 5-FU with F replacing H at C5), and kinase inhibitors (imatinib's ATP-competitive pharmacophore).

Major drug classes and their SAR - drugs acting on body systems

Adrenergics and β-blockers: the catecholamine pharmacophore is a β-phenylethylamine with 3,4-dihydroxy and a β-OH ((R)-configuration required). Increasing N-substituent size shifts α → β selectivity (noradrenaline → adrenaline → isoprenaline). Blockers replace the catechol with an aryloxypropanolamine: propranolol (naphthalene, non-selective), atenolol and metoprolol (para-substituted benzene, β₁-selective), the isopropyl/tert-butyl N-substituent and the (S)-OH being essential.
Cholinergics: acetylcholine's 5-atom rule and quaternary N; carbachol resists cholinesterase; atropine/hyoscine are muscarinic antagonists needing a bulky aromatic acyl group and an ester-linked basic nitrogen.
Histamine H1 antagonists: Ar₂CH−X−CH₂CH₂−N(CH₃)₂ general structure (X = O in diphenhydramine, N in antihistamine ethylenediamines, C in pheniramine); second-generation agents (cetirizine, loratadine, fexofenadine) carry a carboxylate or bulky polar group that keeps them out of the CNS.
H2 antagonists: cimetidine from histamine by adding a cyanoguanidine side chain; ranitidine (furan) and famotidine (thiazole with sulphamoyl) are more potent and avoid cimetidine's CYP inhibition and antiandrogenic effect. Proton pump inhibitors (omeprazole) are acid-activated prodrugs - the benzimidazole-sulphoxide converts to a sulphenamide that binds H⁺/K⁺-ATPase cysteine.
NSAIDs: salicylates (aspirin, acetyl group essential for irreversible COX acetylation), arylalkanoic acids (ibuprofen, naproxen, diclofenac - an acidic group α to an aryl ring, usually with an (S)-α-methyl; ibuprofen undergoes unidirectional R→S inversion), oxicams (enolic acid), and selective COX-2 inhibitors (celecoxib - a sulphonamide/sulphone on one aryl ring of a vicinal diaryl heterocycle fits the larger COX-2 side pocket).
CNS: benzodiazepines - 5-aryl-1,4-benzodiazepin-2-one; electron-withdrawing substituent at C7 (Cl in diazepam, NO₂ in nitrazepam/clonazepam) increases activity, 2'-halogen on the 5-aryl ring helps, substitution at C6-C9 other than C7 reduces it. Phenothiazines - a three-carbon bridge between the ring N10 and the basic amine is essential (a two-carbon bridge gives antihistaminic promethazine), electron-withdrawing C2 substituent (Cl, CF₃) raises potency; piperazine side chains (trifluoperazine) are most potent. Barbiturates/hydantoins - 5,5-disubstitution with a total of about 6-10 carbons; a free NH is needed for acidity.
Cardiovascular: ACE inhibitors mimic the Ala-Pro dipeptide with a zinc-binding group (captopril's thiol, enalapril's carboxylate, fosinopril's phosphinate); sartans replace the imidazole-acid with a biphenyl tetrazole bioisostere; dihydropyridine calcium channel blockers need a 4-aryl ring orthogonal to a 1,4-DHP ring with ester groups at C3/C5.
Antidiabetics: sulphonylureas (Ar−SO₂−NH−CO−NH−R; a p-substituted aryl and a 3-6 carbon lipophilic R), biguanides (metformin), and gliptins/gliflozins as modern classes.

Drug metabolism as a design tool

Phase I (functionalisation): oxidation by CYP450 (CYP3A4, 2D6, 2C9 most relevant), reduction, hydrolysis - usually increases polarity, and sometimes activates a prodrug.
Phase II (conjugation): glucuronidation, sulphation, acetylation (NAT2 polymorphism - fast/slow acetylators of isoniazid are frequent in Indian populations), glutathione conjugation, methylation, glycine conjugation.
Designing against metabolism: block the metabolic soft spot (fluorine at a para position), remove the labile ester, use steric hindrance, or exploit the pathway deliberately in a prodrug.
Toxic metabolites: paracetamol's NAPQI (detoxified by glutathione; N-acetylcysteine is the antidote), halothane's acyl chloride.

Indian regulatory, pharmacopoeial and IP framework

Drugs and Cosmetics Act, 1940 with the Drugs Rules, 1945, and the New Drugs and Clinical Trials Rules, 2019 (CDSCO/DCGI approval, ethics-committee registration, Schedule Y replaced for new drugs); Schedule M revised good manufacturing practice (phased compliance for small manufacturers extended into 2026 - verify the current deadline before quoting it).
Indian Pharmacopoeia (IP), published by the Indian Pharmacopoeia Commission, Ghaziabad - the legal standard under the Act; IP 2026 (10th edition, released January 2026, in effect from 1 July 2026) is the edition in use, with its amendment lists. Structural identity is confirmed by IR against an IP reference spectrum, and related substances are controlled as named impurities - most are predictable from SAR and degradation chemistry (penicilloic acid, 4-aminophenol in paracetamol, 4-epimers of tetracycline).
ICH Q3A/Q3B (impurities), M7 (mutagenic impurities - nitrosamines, alkyl mesylates), Q1A stability - adopted in Indian industry practice.
Patents Act, 1970 (as amended 2005), section 3(d): a new form of a known substance is not patentable unless it shows enhanced therapeutic efficacy - established by the Supreme Court in *Novartis v. Union of India* (2013) over imatinib mesylate β-crystalline form. This is why Indian SAR work focuses on genuinely new chemical entities or demonstrated efficacy gains.
NDPS Act, 1985 governs narcotic and psychotropic classes; Schedule H/H1/X control dispensing of antibiotics, habit-forming drugs and psychotropics.

Key points

SAR - correlating stepwise structural change with change in biological activity; qualitative, whereas QSAR is quantitative.
Pharmacophore - the essential 3D arrangement of groups; losing any one abolishes activity.
Bioisosterism - swapping groups of similar size/electronics to improve potency, stability or patentability (COOH → tetrazole in losartan).
Lipinski's rule of five - MW ≤ 500, log P ≤ 5, HBD ≤ 5, HBA ≤ 10; a guideline for oral drug-likeness, not a law.
log P optimum - about 1-3 for oral absorption, ~2 for CNS penetration; too high means poor solubility and high protein binding.
Hansch equation - log(1/C) = −k₁(log P)² + k₂ log P + k₃σ + k₄Es + k₅; parabolic in lipophilicity.
Sulphonamide SAR - free p-NH₂ essential, N1-heteroaryl improves potency, N4-substitution kills activity.
Penicillin SAR - intact strained β-lactam plus free 3-COOH essential; α-amino side chain broadens the spectrum, bulky ortho-aryl resists penicillinase.
Fluoroquinolone SAR - 3-COOH and 4-oxo essential, 6-F raises potency, 7-piperazine widens the spectrum.
β-Blocker SAR - aryloxypropanolamine with a bulky N-alkyl group; (S)-enantiomer is the eutomer; para-substituted benzene gives β₁ selectivity.
Benzodiazepine SAR - 7-electron-withdrawing group and 5-aryl ring (2'-halogen favourable) are the key potency determinants.
Phenothiazine SAR - three-carbon bridge for antipsychotic action, two-carbon for antihistaminic; C2 electron-withdrawing group raises potency.
NSAID SAR - an acidic centre adjacent to a lipophilic aryl system; COX-2 selectivity comes from a sulphonamide/sulphone on a vicinal diaryl heterocycle.
Prodrug - inactive bio-reversible derivative (enalapril, sulfasalazine, fosphenytoin, chloramphenicol palmitate).
Stereochemistry matters - eutomer/distomer; levofloxacin, (S)-propranolol, (S,S)-ethambutol.
Phase I vs Phase II - functionalisation (CYP450) vs conjugation; NAT2 acetylator status alters isoniazid dosing risk.
Section 3(d), Patents Act - new salt/polymorph patentable only with enhanced therapeutic efficacy (*Novartis v. UOI*, 2013).
Indian Pharmacopoeia - the statutory standard; named related substances are the degradation products SAR predicts.

Formulas and examples

log P = log₁₀ ( C_octanol / C_water ) - partition coefficient, unitless; measured on the unionised species
π_X = log P(R−X) − log P(R−H) - Hansch hydrophobic substituent constant, unitless
σ_X = log K_X − log K_H (benzoic acid ionisation) - Hammett electronic constant, unitless
log (1/C) = −k₁ (log P)² + k₂ (log P) + k₃ σ + k₄ E_s + k₅ - Hansch QSAR; C = molar concentration (mol/L) for a fixed biological response
% unionised (weak acid) = 100 / (1 + 10^{pH − pKa}); % unionised (weak base) = 100 / (1 + 10^{pKa − pH})
pH = pKa + log ([ionised]/[unionised]) for an acid - Henderson-Hasselbalch
Eudismic ratio = Activity(eutomer) / Activity(distomer); Eudismic index = log of that ratio
Ligand efficiency LE = 1.37 × pIC₅₀ / (number of heavy atoms) - kcal/mol per heavy atom
pIC₅₀ = −log₁₀ (IC₅₀ in mol/L)

Example 1 - ionisation and site of absorption (aspirin). Aspirin pKa = 3.5. In gastric fluid at pH 1.5: % unionised = 100/(1 + 10^{1.5 − 3.5}) = 100/(1 + 10⁻²) = 100/1.01 = 99.0% - well absorbed from the stomach. In the jejunum at pH 6.5: 100/(1 + 10^{6.5 − 3.5}) = 100/1001 = 0.0999% unionised. Yet most absorption still occurs in the intestine because its surface area is far larger - the pH-partition hypothesis gives the trend, not the whole answer.

Example 2 - log P from measured concentrations. A candidate distributes between equal volumes of octanol and water: 0.0180 mol/L in octanol and 0.000225 mol/L in water. Ratio = 0.0180/0.000225 = 80 → log P = log 80 = 1.90. MW = 312, HBD = 2, HBA = 5 → all four Lipinski criteria met (MW ≤ 500, log P ≤ 5, HBD ≤ 5, HBA ≤ 10), so 0 violations - good oral prospects.

Example 3 - Hansch prediction. For a series of substituted anilides, log(1/C) = −0.42(log P)² + 1.68(log P) + 0.72σ + 2.10. For a 4-Cl analogue with log P = 2.40 and σ = 0.23: −0.42 × (2.40)² = −0.42 × 5.76 = −2.419; 1.68 × 2.40 = 4.032; 0.72 × 0.23 = 0.166. log(1/C) = −2.419 + 4.032 + 0.166 + 2.10 = 3.879 → C = 10^−3.879 = 1.32 × 10⁻⁴ mol/L. Optimum lipophilicity: d/d(log P) = 0 → log P₀ = 1.68/(2 × 0.42) = 2.00, so this analogue is slightly past the optimum.

Example 4 - eudismic ratio. (S)-propranolol IC₅₀ = 12 nmol/L, (R)-propranolol IC₅₀ = 1,200 nmol/L. Eudismic ratio = 1,200/12 = 100; eudismic index = log 100 = 2.0. pIC₅₀ of the eutomer = −log(12 × 10⁻⁹) = 7.92. With 19 heavy atoms (C₁₆H₂₁NO₂), LE = 1.37 × 7.92/19 = 0.571 kcal/mol per heavy atom - comfortably above the 0.3 benchmark used in lead selection.

Example 5 - prodrug conversion. Enalapril maleate 10 mg (MW of the free base 376.4; maleate salt 492.5) is hydrolysed to enalaprilat (MW 348.4). Free base in a 10 mg salt dose = 10 × 376.4/492.5 = 7.64 mg. Moles = 7.64/376.4 = 0.0203 mmol → enalaprilat formed = 0.0203 × 348.4 = 7.07 mg at complete conversion; actual bioactivation is roughly 60%, so about 4.2 mg of active diacid is generated.

Class	Essential pharmacophore	Change that boosts activity	Change that abolishes activity
Sulphonamides	p-NH₂ + SO₂NH, para relationship	N1-heteroaryl (pKa 6-7.5)	N4-acylation/alkylation (unless cleaved in vivo)
Penicillins	Strained β-lactam + 3-COOH	α-NH₂ side chain; bulky ortho-aryl	Ring opening to penicilloic acid
Fluoroquinolones	3-COOH + 4-oxo	6-F, 7-piperazine	Esterifying the 3-COOH
β-Blockers	Aryloxypropanolamine, (S)-OH	Bulky N-isopropyl/tert-butyl; para-substituent	Loss of the β-OH or N-H
Benzodiazepines	5-aryl-1,4-benzodiazepin-2-one	7-Cl or 7-NO₂; 2'-halo aryl	Saturating/substituting elsewhere on the benzo ring
NSAIDs (arylalkanoic)	Aryl + acidic group, (S)-α-methyl	Second lipophilic ring; 2-naphthyl	Neutralising the carboxylic acid permanently

Parameter	Measures	Typical descriptor	Use in SAR
Lipophilic	Membrane transfer	log P, π	Absorption, CNS entry
Electronic	Charge distribution	σ, pKa, dipole moment	Binding, ionisation
Steric	Bulk and shape	Es, MR, molar volume	Fit in the binding pocket

Where it is used

Formulation and process R&D at Sun Pharma, Cipla, Dr Reddy's, Lupin, Zydus, Torrent, Alkem - salt and polymorph selection, forced-degradation prediction, excipient-drug incompatibility (amine drugs with lactose, the Maillard reaction).
Analytical development and QC - predicting and identifying related substances/impurities for IP, BP, USP and ICH Q3A monographs; justifying specifications in ANDA and DMF filings for US FDA and EU markets.
Discovery chemistry and CRO/CDMO roles at Syngene, Jubilant Biosys, Sai Life Sciences, Aragen, GVK/Aragen and Piramal Pharma Solutions - lead optimisation, SAR tables, scaffold hopping.
Regulatory affairs and IP - section 3(d) arguments, patent landscaping, drafting CTD Module 3 structural sections for CDSCO and foreign agencies.
Clinical pharmacy and medical affairs - explaining drug interactions (fluoroquinolone-antacid chelation, CYP3A4 inhibition by clarithromycin) and dose adjustment in slow acetylators.
Academia and competitive exams - GPAT, NIPER-JEE, GATE-PH, CSIR-UGC NET, and drug inspector/pharmacist recruitment under state PSCs.

Interview questions

Q: What is the difference between SAR and QSAR? A: SAR is a qualitative, observational link between a structural change and the change in activity; QSAR expresses activity as a mathematical function of physicochemical descriptors such as log P, σ and Es, allowing prediction before synthesis.
Q: Why is penicillin G destroyed by stomach acid while penicillin V and ampicillin survive? A: The side-chain in penicillin G is electron-donating, so the β-lactam carbonyl is more prone to acid-catalysed attack; the electron-withdrawing phenoxymethyl (V) and α-amino (ampicillin) side chains reduce that attack on the ring.
Q: Why does substituting the N4-amino group of sulphanilamide destroy activity, yet prontosil works? A: The free p-amino group is essential for PABA mimicry; prontosil is a prodrug whose azo link is reduced by gut bacteria to release sulphanilamide in vivo.
Q: Give one textbook example of bioisosteric replacement that mattered commercially. A: Replacing the carboxylic acid of early angiotensin antagonists with a tetrazole gave losartan - similar acidity and charge, but better lipophilicity, metabolic stability and oral bioavailability.
Q: How does a three-carbon versus two-carbon bridge change phenothiazine action? A: A three-carbon bridge between N10 and the basic nitrogen gives antipsychotic (dopamine-blocking) activity, as in chlorpromazine; a two-carbon bridge gives antihistaminic activity, as in promethazine.
Q: What makes a COX-2 inhibitor selective? A: COX-2's active site has an extra side pocket; a vicinal diaryl heterocycle bearing a sulphonamide or methylsulphone (celecoxib, rofecoxib) fits that pocket, which the narrower COX-1 site cannot accept.
Q: Why is only the (S)-enantiomer of ofloxacin marketed as levofloxacin? A: The (S)-form carries essentially all the gyrase-inhibitory activity, so using it halves the dose and the burden of inactive material; the (R)-form is the distomer.
Q: What is a prodrug, and name four with different design goals. A: A bio-reversible inactive derivative converted in vivo to the active drug - enalapril (absorption), chloramphenicol palmitate (taste), sulfasalazine (colonic targeting) and fosphenytoin (water solubility for injection).
Q: State Lipinski's rule of five and one important limitation. A: MW ≤ 500, log P ≤ 5, H-bond donors ≤ 5, acceptors ≤ 10 predict oral drug-likeness; it does not apply to actively transported or natural-product-derived drugs (many antibiotics, statins and cyclosporine violate it and still work orally).
Q: How does section 3(d) of the Patents Act affect Indian medicinal chemistry? A: A new salt, ester, polymorph or isomer of a known substance is not patentable unless enhanced therapeutic efficacy is proved - upheld by the Supreme Court in the Novartis imatinib mesylate case in 2013 - so incremental changes must deliver a demonstrated clinical gain.
Q: Why does ciprofloxacin fail if taken with antacids or milk? A: The 3-carboxyl and 4-oxo groups chelate di- and trivalent cations (Ca²⁺, Mg²⁺, Al³⁺, Fe²⁺), forming insoluble complexes that are not absorbed.
Q: How is metabolism used deliberately in drug design? A: Either by blocking a metabolic soft spot (introducing fluorine or steric bulk to extend half-life) or by exploiting it - prodrugs rely on hydrolysis or CYP activation, as with cyclophosphamide's CYP2B6 activation.

Common mistakes

Treating SAR as if structure alone decides activity - ignoring pharmacokinetics, so a potent molecule with log P 7 is proposed as an oral drug.
Quoting Lipinski's rule of five as a pass/fail law rather than a guideline, and forgetting that it says nothing about potency or toxicity.
Mixing up the Henderson-Hasselbalch forms for acids and bases, and reporting the ionised fraction as the unionised one.
Forgetting that pIC₅₀ needs IC₅₀ in mol/L - using nmol/L or µg/mL gives an answer wrong by several log units.
Saying any β-lactam ring gives antibacterial action; without the free 3-carboxyl, correct stereochemistry and ring strain there is no transpeptidase acylation.
Confusing isosteres with bioisosteres, or assuming a bioisosteric swap always preserves activity - it can reverse it (5-FU versus uracil).
Ignoring stereochemistry: writing "propranolol" or "ethambutol" without noting that one enantiomer carries the activity, and mislabelling a racemate's potency.
Reciting generations of cephalosporins or quinolones without the structural reason for the change in spectrum - interviewers ask "why", not "list".