## 8 How Small Molecules Inhibit RNA Transcription  
Bacterial RNAP is essential for cell growth and viability, and lack of sequence and structural similarities between certain areas of bacterial and eukaryotic RNAP make this enzyme an attractive target for antibiotic development. Crystal structures of bacterial RNAP in complex with small molecule transcription inhibitors have been used to characterize binding sites, mechanisms of action, and mechanisms of resistance (Table 3 and Figure 3). Currently, two bacterial RNAP inhibitors, rifampicin (also known as rifampicin) and fidaxomicin (also known as DIFICID(r) and lipiarmycin), have been used in clinical practice. Rifampin, a semisynthetic rifamycin, is the cornerstone of current tuberculosis treatment. Structures of the RNAP-rifampin complex (_T. aquatic_s core enzyme, PDB: 1 YNN; _E. coli_ holoenzyme,PDB: 4 KMU) provided a detailed view of the interaction between rifampin and the \(\beta\) subunit and explained how rifampicin blocks RNA extension [80,81]. The rifampin binding site is also recognized by sornagicin, which prevents extension of short RNA (PDB: 1 YNJ) [82]. Chemical modifications of rifampin have provided an additional RNAP-drug interface that may enhance drug affinity and efficacy, as well as reduce the frequency of spontaneous resistance mutations. Structures of RNAP holoenzymes in complex with rifampicin derivatives (_T. thermophiles_ holoenzyme, PDB: 2A68, 2A69; _E. coli_ holoenzyme, PDB: 4 KN4, 4 KN7) showed an additional interaction with the \(\sigma\) region 3.2 (\(\sigma\) finger) that may influence binding of template DNA at the active site, thereby reducing the efficiency of transcription initiation [81,83]. The structure of RNAP in complex with GE23077 (PDB: 4 MQ9, 4 OIN, 4 OIP), a drug that inhibits nucleotide binding, provided a framework for creating a bipartite compound by tethering rifampin with GE23077, which has superior affinities for both rifampin-susceptible and rifampin-resistant RNAPs (PDB: 4 OIR) [41]. Stretpolyl digin binds to key elements of the RNAP active site (bridge helix and trigger loop) and inhibits all reactions involved in RNAP transcription by blocking conformational changes in these elements that occur during transcription. Structures of the RNAP-stretpolyl digin complex revealed that it traps the bridge helix and trigger loop in straight and unfolded conformational states, respectively, by direct interaction with these elements (PDB: 2 PPB, 1 ZYR, 2A6H) [34,42,84]. Myxopyronin binds to the RNAP switch region, which is a hinge of the RNAP clamp whose function is to open and close the DNA-binding channel. Upon binding, myxopyronin inhibits transcript initiation by preventing formation of the promoter open complex. Structural and biochemical studies on the _T. thermophilus_ RNAP-myxopyronin complex (PDB: 3 DXJ, 3 EQL) have proposed two models of \begin{table}
\begin{tabular}{l l l l} \hline
**Structure** & **PDB** & **Reference** & **Source** \\ \hline Core enzyme–rifampin & 1 YNN & [80] & B \\ Holoenzyme–rifampin & 4 KMU & [81] & A \\ Holoenzyme–rifampin derivatives & 2A68, 2A69 & [83] & B \\ Holoenzyme–rifampin derivatives & 4 KN4, 4 KN7 & [81] & A \\ Holoenzyme–ppGpp & 1 SMY & [76] & B \\ Holoenzyme–ppGpp & 4 JK1, 4 JKR & [74,75] & A \\ Holoenzyme–ppppGpp & 4 JK2 & [74] & A \\ Core enzyme–sorangicin & 1 YNJ & [82] & B \\ Holoenzyme–stretpolyl digin & 1 ZYR, 2A6H & [34,84] & B \\ Elongation complex–stretpolyl digin & 2 PPB & [42] & B \\ Holoenzyme–myxopyronin & 3 DXJ, 3 EQL & [85,86] & B \\ Holoenzyme–myxopyronin & 4 YFX & [87] & A \\ Holoenzyme–GE23077 & 4 MQ9 & [41] & B \\ Holoenzyme–DNA–GE23077 & 4 OIN, 4 OIP & [41] & B \\ Holoenzyme–DNA– & 4 OIR & [41] & B \\ GE23077/rifamycin SV & & & \\ Holoenzyme–sainamide A & 4 MEX & [37] & A \\ Holoenzyme–squaramide & 4 YFK, 4 YFN & [87] & A \\ \hline \end{tabular}  
* A: _Escherichia coli_; B: _Thermus aquatics/Thermusthermophilus_,
* All structures in this table were determined by X-ray crystallography method.  
\end{table}